Browse code

Script to pull most recent upstream CV files, closing #229

Steffen Neumann authored on 09/09/2020 08:29:24
Showing4 changed files

... ...
@@ -151,7 +151,7 @@ const TermInfo termInfos_[] =
151 151
     {MS_minute_OBSOLETE, "MS:1000038", "minute", "Acquisition time in minutes.", true},
152 152
     {MS_second_OBSOLETE, "MS:1000039", "second", "Acquisition time in seconds.", true},
153 153
     {MS_m_z, "MS:1000040", "m/z", "Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.", false},
154
-    {MS_charge_state, "MS:1000041", "charge state", "The charge state of the ion, single or multiple and positive or negatively charged.", false},
154
+    {MS_charge_state, "MS:1000041", "charge state", "Number of net charges, positive or negative, on an ion.", false},
155 155
     {MS_peak_intensity, "MS:1000042", "peak intensity", "Intensity of ions as measured by the height or area of a peak in a mass spectrum.", false},
156 156
     {MS_intensity_unit, "MS:1000043", "intensity unit", "Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors.", false},
157 157
     {MS_dissociation_method, "MS:1000044", "dissociation method", "Fragmentation method used for dissociation or fragmentation.", false},
... ...
@@ -334,7 +334,7 @@ const TermInfo termInfos_[] =
334 334
     {MS_magnetic_deflection, "MS:1000221", "magnetic deflection", "The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer.", false},
335 335
     {MS_mass_defect_OBSOLETE, "MS:1000222", "mass defect", "The difference between the monoisotopic and nominal mass of a molecule or atom.", true},
336 336
     {MS_mass_number_OBSOLETE, "MS:1000223", "mass number", "The sum of the protons and neutrons in an atom, molecule or ion.", true},
337
-    {MS_molecular_mass_OBSOLETE, "MS:1000224", "molecular mass", "The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules).", true},
337
+    {MS_molecular_mass, "MS:1000224", "molecular mass", "Mass of a molecule measured in unified atomic mass units (u or Da).", false},
338 338
     {MS_monoisotopic_mass_OBSOLETE, "MS:1000225", "monoisotopic mass", "The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.", true},
339 339
     {MS_molecular_beam_mass_spectrometry_OBSOLETE, "MS:1000226", "molecular beam mass spectrometry", "A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.", true},
340 340
     {MS_multiphoton_ionization, "MS:1000227", "multiphoton ionization", "Photoionization of an atom or molecule in which in two or more photons are absorbed.", false},
... ...
@@ -551,7 +551,7 @@ const TermInfo termInfos_[] =
551 551
     {MS_surface_induced_reaction_OBSOLETE, "MS:1000439", "surface-induced reaction", "A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion.", true},
552 552
     {MS_unimolecular_dissociation_OBSOLETE, "MS:1000440", "unimolecular dissociation", "Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion.", true},
553 553
     {MS_scan, "MS:1000441", "scan", "Function or process of the mass spectrometer where it records a spectrum.", false},
554
-    {MS_spectrum, "MS:1000442", "spectrum", "A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis.", false},
554
+    {MS_spectrum, "MS:1000442", "spectrum", "Representation of intensity values corresponding to a range of measurement space.", false},
555 555
     {MS_mass_analyzer_type, "MS:1000443", "mass analyzer type", "Mass analyzer separates the ions according to their mass-to-charge ratio.", false},
556 556
     {MS_m_z_Separation_Method_OBSOLETE, "MS:1000444", "m/z Separation Method", "Mass/charge separation Method.", true},
557 557
     {MS_sequential_m_z_separation_method_OBSOLETE, "MS:1000445", "sequential m/z separation method", "Sequential m/z separation method.", true},
... ...
@@ -606,21 +606,21 @@ const TermInfo termInfos_[] =
606 606
     {MS_Thermo_Scientific_instrument_model, "MS:1000494", "Thermo Scientific instrument model", "Thermo Scientific instrument model.", false},
607 607
     {MS_Applied_Biosystems_instrument_model, "MS:1000495", "Applied Biosystems instrument model", "Applied Biosystems instrument model.", false},
608 608
     {MS_instrument_attribute, "MS:1000496", "instrument attribute", "Instrument properties that are associated with a value.", false},
609
-    {MS_zoom_scan, "MS:1000497", "zoom scan", "Special scan mode, where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.", false},
609
+    {MS_zoom_scan, "MS:1000497", "zoom scan", "Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.", false},
610 610
     {MS_full_scan_OBSOLETE, "MS:1000498", "full scan", "Feature of the ion trap mass spectrometer where MS data is acquired over a mass range.", true},
611
-    {MS_spectrum_attribute, "MS:1000499", "spectrum attribute", "Spectrum properties that are associated with a value.", false},
611
+    {MS_spectrum_attribute, "MS:1000499", "spectrum attribute", "Nonphysical characteristic attributed to a spectrum.", false},
612 612
     {MS_scan_window_upper_limit, "MS:1000500", "scan window upper limit", "The lower m/z bound of a mass spectrometer scan window.", false},
613 613
     {MS_scan_window_lower_limit, "MS:1000501", "scan window lower limit", "The upper m/z bound of a mass spectrometer scan window.", false},
614 614
     {MS_dwell_time, "MS:1000502", "dwell time", "The time spent gathering data across a peak.", false},
615
-    {MS_scan_attribute, "MS:1000503", "scan attribute", "Scan properties that are associated with a value.", false},
615
+    {MS_scan_attribute, "MS:1000503", "scan attribute", "Nonphysical characteristic attributed to a spectrum acquisition scan.", false},
616 616
     {MS_base_peak_m_z, "MS:1000504", "base peak m/z", "M/z value of the signal of highest intensity in the mass spectrum.", false},
617 617
     {MS_base_peak_intensity, "MS:1000505", "base peak intensity", "The intensity of the greatest peak in the mass spectrum.", false},
618 618
     {MS_ion_role_OBSOLETE, "MS:1000506", "ion role", "Ion Role.", true},
619
-    {MS_ion_attribute_OBSOLETE, "MS:1000507", "ion attribute", "Ion properties that are associated with a value.", true},
619
+    {MS_ion_property, "MS:1000507", "ion property", "Nonphysical characteristic attributed to an ion.", false},
620 620
     {MS_ion_chemical_type_OBSOLETE, "MS:1000508", "ion chemical type", "Ion Type.", true},
621 621
     {MS_activation_energy, "MS:1000509", "activation energy", "Activation Energy.", false},
622 622
     {MS_precursor_activation_attribute, "MS:1000510", "precursor activation attribute", "Precursor Activation Attribute.", false},
623
-    {MS_ms_level, "MS:1000511", "ms level", "Stages of ms achieved in a multi stage mass spectrometry experiment.", false},
623
+    {MS_ms_level, "MS:1000511", "ms level", "Stage number achieved in a multi stage mass spectrometry acquisition.", false},
624 624
     {MS_filter_string, "MS:1000512", "filter string", "A string unique to Thermo instrument describing instrument settings for the scan.", false},
625 625
     {MS_binary_data_array, "MS:1000513", "binary data array", "A data array of values.", false},
626 626
     {MS_m_z_array, "MS:1000514", "m/z array", "A data array of m/z values.", false},
... ...
@@ -686,7 +686,7 @@ const TermInfo termInfos_[] =
686 686
     {MS_zlib_compression, "MS:1000574", "zlib compression", "Zlib.", false},
687 687
     {MS_mean_of_spectra, "MS:1000575", "mean of spectra", "Spectra is combined by calculating the mean of the spectra.", false},
688 688
     {MS_no_compression, "MS:1000576", "no compression", "No Compression.", false},
689
-    {MS_raw_data_file, "MS:1000577", "raw data file", "Describes the type of file and its content.", false},
689
+    {MS_source_data_file, "MS:1000577", "source data file", "Data file from which an entity is sourced.", false},
690 690
     {MS_LCQ_Fleet, "MS:1000578", "LCQ Fleet", "LCQ Fleet.", false},
691 691
     {MS_MS1_spectrum, "MS:1000579", "MS1 spectrum", "Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.", false},
692 692
     {MS_MSn_spectrum, "MS:1000580", "MSn spectrum", "MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n.", false},
... ...
@@ -904,7 +904,7 @@ const TermInfo termInfos_[] =
904 904
     {MS_isolation_window_upper_limit_OBSOLETE, "MS:1000793", "isolation window upper limit", "The highest m/z being isolated in an isolation window.", true},
905 905
     {MS_isolation_window_lower_limit_OBSOLETE, "MS:1000794", "isolation window lower limit", "The lowest m/z being isolated in an isolation window.", true},
906 906
     {MS_no_combination, "MS:1000795", "no combination", "Use this term if only one scan was recorded or there is no information about scans available.", false},
907
-    {MS_spectrum_title, "MS:1000796", "spectrum title", "A free-form text title describing a spectrum.", false},
907
+    {MS_spectrum_title, "MS:1000796", "spectrum title", "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file.", false},
908 908
     {MS_peak_list_scans, "MS:1000797", "peak list scans", "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.", false},
909 909
     {MS_peak_list_raw_scans, "MS:1000798", "peak list raw scans", "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.", false},
910 910
     {MS_custom_unreleased_software_tool, "MS:1000799", "custom unreleased software tool", "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added.", false},
... ...
@@ -966,16 +966,16 @@ const TermInfo termInfos_[] =
966 966
     {MS_LTQ_Velos_ETD, "MS:1000856", "LTQ Velos ETD", "Thermo Scientific LTQ Velos MS with ETD.", false},
967 967
     {MS_run_attribute, "MS:1000857", "run attribute", "Properties of the described run.", false},
968 968
     {MS_fraction_identifier, "MS:1000858", "fraction identifier", "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information.", false},
969
-    {MS_molecule, "MS:1000859", "molecule", "A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.", false},
970
-    {MS_peptide, "MS:1000860", "peptide", "A compound of low molecular weight that is composed of two or more amino acids.", false},
971
-    {MS_chemical_compound_attribute, "MS:1000861", "chemical compound attribute", "A describable property of a chemical compound.", false},
969
+    {MS_molecule, "MS:1000859", "molecule", "Group of two or more atoms held together by chemical bonds.", false},
970
+    {MS_peptide, "MS:1000860", "peptide", "A molecule of low molecular weight that is composed of two or more amino acid residues.", false},
971
+    {MS_molecular_entity_property, "MS:1000861", "molecular entity property", "A physical characteristic of a molecular entity.", false},
972 972
     {MS_isoelectric_point, "MS:1000862", "isoelectric point", "The pH of a solution at which a charged molecule does not migrate in an electric field.", false},
973 973
     {MS_predicted_isoelectric_point, "MS:1000863", "predicted isoelectric point", "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.", false},
974
-    {MS_chemical_compound_formula, "MS:1000864", "chemical compound formula", "A combination of symbols used to express the chemical composition of a compound.", false},
974
+    {MS_chemical_formula, "MS:1000864", "chemical formula", "A combination of symbols used to express the chemical composition of a molecule.", false},
975 975
     {MS_empirical_formula, "MS:1000865", "empirical formula", "A chemical formula which expresses the proportions of the elements present in a substance.", false},
976 976
     {MS_molecular_formula, "MS:1000866", "molecular formula", "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.", false},
977 977
     {MS_structural_formula, "MS:1000867", "structural formula", "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.", false},
978
-    {MS_SMILES_string, "MS:1000868", "SMILES string", "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.", false},
978
+    {MS_SMILES_formula, "MS:1000868", "SMILES formula", "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.", false},
979 979
     {MS_collision_gas_pressure, "MS:1000869", "collision gas pressure", "The gas pressure of the collision gas used for collisional excitation.", false},
980 980
     {MS_4000_QTRAP_OBSOLETE, "MS:1000870", "4000 QTRAP", "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000.", true},
981 981
     {MS_SRM_software, "MS:1000871", "SRM software", "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.", false},
... ...
@@ -988,19 +988,19 @@ const TermInfo termInfos_[] =
988 988
     {MS_external_reference_identifier, "MS:1000878", "external reference identifier", "An identifier/accession number to an external reference database.", false},
989 989
     {MS_PubMed_identifier, "MS:1000879", "PubMed identifier", "A unique identifier for a publication in the PubMed database (MIR:00000015).", false},
990 990
     {MS_interchannel_delay, "MS:1000880", "interchannel delay", "The duration of intervals between scanning, during which the instrument configuration is switched.", false},
991
-    {MS_chemical_compound, "MS:1000881", "chemical compound", "A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.", false},
992
-    {MS_protein, "MS:1000882", "protein", "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.", false},
991
+    {MS_molecular_entity, "MS:1000881", "molecular entity", "Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.", false},
992
+    {MS_protein, "MS:1000882", "protein", "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene.", false},
993 993
     {MS_protein_short_name, "MS:1000883", "protein short name", "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).", false},
994
-    {MS_protein_attribute, "MS:1000884", "protein attribute", "An nonphysical attribute describing a specific protein.", false},
995
-    {MS_protein_accession, "MS:1000885", "protein accession", "Accession number for a specific protein in a database.", false},
994
+    {MS_protein_attribute, "MS:1000884", "protein attribute", "An nonphysical characterstic attributed to a specific protein.", false},
995
+    {MS_protein_accession, "MS:1000885", "protein accession", "Identifier for a specific protein in a database.", false},
996 996
     {MS_protein_name, "MS:1000886", "protein name", "A long name describing the function of the protein.", false},
997
-    {MS_peptide_attribute, "MS:1000887", "peptide attribute", "A nonphysical attribute that can be used to describe a peptide.", false},
998
-    {MS_unmodified_peptide_sequence, "MS:1000888", "unmodified peptide sequence", "A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.", false},
999
-    {MS_modified_peptide_sequence, "MS:1000889", "modified peptide sequence", "A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid modifications that are present.", false},
1000
-    {MS_peptide_labeling_state, "MS:1000890", "peptide labeling state", "A state description of how a peptide might be isotopically or isobarically labelled.", false},
1001
-    {MS_heavy_labeled_peptide, "MS:1000891", "heavy labeled peptide", "A peptide that has been created or labelled with some heavier-than-usual isotopes.", false},
1002
-    {MS_unlabeled_peptide, "MS:1000892", "unlabeled peptide", "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \\\"light\\\" to distinguish from \\\"heavy\\\".", false},
1003
-    {MS_peptide_group_label, "MS:1000893", "peptide group label", "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.", false},
997
+    {MS_peptide_attribute, "MS:1000887", "peptide attribute", "Nonphysical characteristic attributed to a peptide.", false},
998
+    {MS_stripped_peptide_sequence, "MS:1000888", "stripped peptide sequence", "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away.", false},
999
+    {MS_peptidoform_sequence, "MS:1000889", "peptidoform sequence", "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present.", false},
1000
+    {MS_peptidoform_labeling_state, "MS:1000890", "peptidoform labeling state", "A state description of how a peptide might be isotopically or isobarically labelled.", false},
1001
+    {MS_heavy_labeled_peptidoform, "MS:1000891", "heavy labeled peptidoform", "A peptide that has been created or labelled with some heavier-than-usual isotopes.", false},
1002
+    {MS_unlabeled_peptidoform, "MS:1000892", "unlabeled peptidoform", "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \\\"light\\\" to distinguish from \\\"heavy\\\".", false},
1003
+    {MS_peptidoform_group_label, "MS:1000893", "peptidoform group label", "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.", false},
1004 1004
     {MS_retention_time, "MS:1000894", "retention time", "A time interval from the start of chromatography when an analyte exits a chromatographic column.", false},
1005 1005
     {MS_local_retention_time, "MS:1000895", "local retention time", "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup.", false},
1006 1006
     {MS_normalized_retention_time, "MS:1000896", "normalized retention time", "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup.", false},
... ...
@@ -1136,8 +1136,8 @@ const TermInfo termInfos_[] =
1136 1136
     {MS_SEQUEST_CullTo, "MS:1001109", "SEQUEST:CullTo", "Specify cull string as value of the CVParam.", false},
1137 1137
     {MS_SEQUEST_modeCV, "MS:1001110", "SEQUEST:modeCV", "SEQUEST Mode Input Parameters.", false},
1138 1138
     {MS_SEQUEST_Full, "MS:1001111", "SEQUEST:Full", "", false},
1139
-    {MS_n_terminal_flanking_residue, "MS:1001112", "n-terminal flanking residue", "The residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.", false},
1140
-    {MS_c_terminal_flanking_residue, "MS:1001113", "c-terminal flanking residue", "The residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.", false},
1139
+    {MS_n_terminal_flanking_residue, "MS:1001112", "n-terminal flanking residue", "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.", false},
1140
+    {MS_c_terminal_flanking_residue, "MS:1001113", "c-terminal flanking residue", "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.", false},
1141 1141
     {MS_retention_time_s__OBSOLETE, "MS:1001114", "retention time(s)", "Retention time of the spectrum from the source file.", true},
1142 1142
     {MS_scan_number_s__OBSOLETE, "MS:1001115", "scan number(s)", "OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData.", true},
1143 1143
     {MS_single_protein_identification_statistic, "MS:1001116", "single protein identification statistic", "Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group).", false},
... ...
@@ -1905,7 +1905,7 @@ const TermInfo termInfos_[] =
1905 1905
     {MS_retention_time_window_width, "MS:1001907", "retention time window width", "The full width of a retention time window for a chromatographic peak.", false},
1906 1906
     {MS_ISQ, "MS:1001908", "ISQ", "Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source.", false},
1907 1907
     {MS_Velos_Plus, "MS:1001909", "Velos Plus", "Thermo Scientific second generation Velos.", false},
1908
-    {MS_LTQ_Orbitrap_Elite, "MS:1001910", "LTQ Orbitrap Elite", "Thermo Scientific second generation Velos and Orbitrap.", false},
1908
+    {MS_LTQ_Orbitrap_Elite, "MS:1001910", "LTQ Orbitrap Elite", "Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite.", false},
1909 1909
     {MS_Q_Exactive, "MS:1001911", "Q Exactive", "Thermo Scientific Q Exactive.", false},
1910 1910
     {MS_PinPoint, "MS:1001912", "PinPoint", "Thermo Scientific PinPoint SRM analysis software.", false},
1911 1911
     {MS_S_lens_voltage, "MS:1001913", "S-lens voltage", "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts.", false},
... ...
@@ -2786,22 +2786,22 @@ const TermInfo termInfos_[] =
2786 2786
     {MS_7000B_Triple_Quadrupole_GC_MS, "MS:1002803", "7000B Triple Quadrupole GC/MS", "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.", false},
2787 2787
     {MS_7800_Quadrupole_ICP_MS, "MS:1002804", "7800 Quadrupole ICP-MS", "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer.", false},
2788 2788
     {MS_8800_Triple_Quadrupole_ICP_MS, "MS:1002805", "8800 Triple Quadrupole ICP-MS", "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer.", false},
2789
-    {MS_ion, "MS:1002806", "ion", "An atomic or molecular species having a net positive or negative electric charge.", false},
2789
+    {MS_ion, "MS:1002806", "ion", "Molecular entity having a net positive or negative electric charge.", false},
2790 2790
     {MS_positive_mode_adduct_ion, "MS:1002807", "positive mode adduct ion", "Adduct ion with positive ionization.", false},
2791 2791
     {MS_negative_mode_adduct_ion, "MS:1002808", "negative mode adduct ion", "Adduct ion with negative ionization.", false},
2792
-    {MS_adduct_ion_attribute, "MS:1002809", "adduct ion attribute", "Attribute describing an adduct formation.", false},
2793
-    {MS_adduct_ion_mass, "MS:1002810", "adduct ion mass", "Mass of an adduct formation specified by the given value.", false},
2792
+    {MS_adduct_ion_attribute, "MS:1002809", "adduct ion attribute", "Nonphysical characteristic attributed to an adduct ion.", false},
2793
+    {MS_adduct_ion_X_m_z, "MS:1002810", "adduct ion X m/z", "Theoretical m/z of the X component in the adduct M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator.", false},
2794 2794
     {MS_adduct_ion_isotope, "MS:1002811", "adduct ion isotope", "Isotope of the matrix molecule M of an adduct formation.", false},
2795 2795
     {MS_Regular_expression_for_adduct_ion_formula, "MS:1002812", "Regular expression for adduct ion formula", "(\\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\\][:digit:]{0,1}[+-]).", false},
2796
-    {MS_adduct_ion_formula, "MS:1002813", "adduct ion formula", "Adduct formation formula specified by the given value.", false},
2796
+    {MS_adduct_ion_formula, "MS:1002813", "adduct ion formula", "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression.", false},
2797 2797
     {MS_volt_second_per_square_centimeter, "MS:1002814", "volt-second per square centimeter", "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm].", false},
2798 2798
     {MS_inverse_reduced_ion_mobility, "MS:1002815", "inverse reduced ion mobility", "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated.", false},
2799 2799
     {MS_mean_ion_mobility_array, "MS:1002816", "mean ion mobility array", "Array of drift times, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array.", false},
2800 2800
     {MS_Bruker_TDF_format, "MS:1002817", "Bruker TDF format", "Bruker TDF raw file format.", false},
2801 2801
     {MS_Bruker_TDF_nativeID_format, "MS:1002818", "Bruker TDF nativeID format", "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.", false},
2802 2802
     {MS_Bruker_TDF_nativeID_format__combined_spectra, "MS:1002819", "Bruker TDF nativeID format, combined spectra", "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation.", false},
2803
-    {MS_M_H_ion_1002820, "MS:1002820", "M+H ion (MS:1002820)", "M+H ion from positive ion mode (M in the property ionMass denotes the mass of the neutral molecule).", false},
2804
-    {MS_M_H_ion_1002821, "MS:1002821", "M-H ion (MS:1002821)", "M-H ion from negative ion mode (M in the property ionMass denotes the mass of the neutral molecule).", false},
2803
+    {MS_M_H_ion_1002820, "MS:1002820", "M+H ion (MS:1002820)", "Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton.", false},
2804
+    {MS_M_H_ion_1002821, "MS:1002821", "M-H ion (MS:1002821)", "Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M.", false},
2805 2805
     {MS_OpenMS_file_format, "MS:1002822", "OpenMS file format", "File format developed by the OpenMS team.", false},
2806 2806
     {MS_idXML, "MS:1002823", "idXML", "OpenMS intermediate identification format.", false},
2807 2807
     {MS_featureXML, "MS:1002824", "featureXML", "OpenMS feature file format.", false},
... ...
@@ -2836,8 +2836,8 @@ const TermInfo termInfos_[] =
2836 2836
     {MS_Dataset_with_no_associated_published_manuscript, "MS:1002853", "Dataset with no associated published manuscript", "A dataset which does not have an associated published manuscript.", false},
2837 2837
     {MS_Peer_reviewed_dataset, "MS:1002854", "Peer-reviewed dataset", "Dataset has been peer-reviewed somehow.", false},
2838 2838
     {MS_Non_peer_reviewed_dataset, "MS:1002855", "Non peer-reviewed dataset", "Dataset that has not been peer-reviewed by any means.", false},
2839
-    {MS_Supported_dataset_by_repository, "MS:1002856", "Supported dataset by repository", "The PX dataset is supported by and is available through the submission repository.", false},
2840
-    {MS_Unsupported_dataset_by_repository, "MS:1002857", "Unsupported dataset by repository", "The PX dataset is not fully supported by the submission repository.", false},
2839
+    {MS_Supported_dataset_by_repository, "MS:1002856", "Supported dataset by repository", "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission.", false},
2840
+    {MS_Unsupported_dataset_by_repository, "MS:1002857", "Unsupported dataset by repository", "Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission.", false},
2841 2841
     {MS_Dataset_with_its_publication_pending, "MS:1002858", "Dataset with its publication pending", "A dataset which has an associated manuscript pending for publication.", false},
2842 2842
     {MS_Additional_associated_raw_file_URI, "MS:1002859", "Additional associated raw file URI", "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE.", false},
2843 2843
     {MS_Gel_image_file_URI, "MS:1002860", "Gel image file URI", "URI of one gel image file associated to one PX submission.", false},
... ...
@@ -2992,7 +2992,7 @@ const TermInfo termInfos_[] =
2992 2992
     {MS_KSDP_score, "MS:1003012", "KSDP score", "Kernel mass spectral dot product scoring function.", false},
2993 2993
     {MS_i3tms, "MS:1003013", "i3tms", "i3-tms search engine and data-analysis software.", false},
2994 2994
     {MS_MSFragger, "MS:1003014", "MSFragger", "A database search-based peptide identification tool.", false},
2995
-    {MS_razor_peptide, "MS:1003015", "razor peptide", "A peptide which is shared between protein groups and assigned to the protein group with the largest number of identified peptides.", false},
2995
+    {MS_razor_peptide, "MS:1003015", "razor peptide", "Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides.", false},
2996 2996
     {MS_ProteinProphet_peptide_weight, "MS:1003016", "ProteinProphet:peptide weight", "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins.", false},
2997 2997
     {MS_ProteinProphet_peptide_group_weight, "MS:1003017", "ProteinProphet:peptide group weight", "Fraction of peptide evidence attributable to a group of proteins.", false},
2998 2998
     {MS_Philosopher, "MS:1003018", "Philosopher", "General proteomics processing toolkit for shotgun proteomics.", false},
... ...
@@ -3008,6 +3008,88 @@ const TermInfo termInfos_[] =
3008 3008
     {MS_Orbitrap_Exploris_480, "MS:1003028", "Orbitrap Exploris 480", "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS.", false},
3009 3009
     {MS_Orbitrap_Eclipse, "MS:1003029", "Orbitrap Eclipse", "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.", false},
3010 3010
     {MS_Mascot_MinNumSigUniqueSeqs, "MS:1003030", "Mascot:MinNumSigUniqueSeqs", "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'.", false},
3011
+    {MS_CPTAC_accession_number, "MS:1003031", "CPTAC accession number", "Main identifier of a CPTAC dataset.", false},
3012
+    {MS_compound_identification_confidence_code_in_MS_DIAL, "MS:1003032", "compound identification confidence code in MS-DIAL", "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program.", false},
3013
+    {MS_molecular_entity_attribute, "MS:1003033", "molecular entity attribute", "Non-inherent characteristic attributed to a molecular entity.", false},
3014
+    {MS_atom, "MS:1003034", "atom", "Smallest constituent unit of ordinary matter that constitutes a chemical element.", false},
3015
+    {MS_small_molecule, "MS:1003035", "small molecule", "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process.", false},
3016
+    {MS_metabolite, "MS:1003036", "metabolite", "Small molecule that is the intermediate end product of metabolism.", false},
3017
+    {MS_ribonucleotide, "MS:1003037", "ribonucleotide", "Nucleotide containing ribose as its pentose component.", false},
3018
+    {MS_deoxyribonucleotide, "MS:1003038", "deoxyribonucleotide", "Monomer, or single unit, of DNA, or deoxyribonucleic acid.", false},
3019
+    {MS_amino_acid, "MS:1003039", "amino acid", "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid.", false},
3020
+    {MS_monosaccharide, "MS:1003040", "monosaccharide", "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule.", false},
3021
+    {MS_nucleic_acid, "MS:1003041", "nucleic acid", "Molecule composed of a chain of nucleotides.", false},
3022
+    {MS_polysaccharide, "MS:1003042", "polysaccharide", "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages.", false},
3023
+    {MS_number_of_residues, "MS:1003043", "number of residues", "Number of amino acid residues in a peptide, commonly referred to as the peptide length.", false},
3024
+    {MS_number_of_missed_cleavages, "MS:1003044", "number of missed cleavages", "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not.", false},
3025
+    {MS_peptide_to_protein_mapping, "MS:1003045", "peptide-to-protein mapping", "Process of mapping a peptide sequence to a protein sequence.", false},
3026
+    {MS_peptide_to_protein_mapping_attribute, "MS:1003046", "peptide-to-protein mapping attribute", "Nonphysical characteristic attributed to the result of peptide-to-protein mapping.", false},
3027
+    {MS_protein_sequence_offset, "MS:1003047", "protein sequence offset", "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence.", false},
3028
+    {MS_number_of_enzymatic_termini, "MS:1003048", "number of enzymatic termini", "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules.", false},
3029
+    {MS_peptidoform, "MS:1003049", "peptidoform", "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations.", false},
3030
+    {MS_peptidoform_attribute, "MS:1003050", "peptidoform attribute", "Non-inherent characteristic attributed to a peptidoform.", false},
3031
+    {MS_peptidoform_ion, "MS:1003051", "peptidoform ion", "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'.", false},
3032
+    {MS_peptidoform_ion_property, "MS:1003052", "peptidoform ion property", "Inherent or measurable characteristic of a peptidoform ion.", false},
3033
+    {MS_theoretical_monoisotopic_m_z, "MS:1003053", "theoretical monoisotopic m/z", "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents.", false},
3034
+    {MS_theoretical_average_m_z, "MS:1003054", "theoretical average m/z", "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes.", false},
3035
+    {MS_adduct, "MS:1003055", "adduct", "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species.", false},
3036
+    {MS_adduct_ion_property, "MS:1003056", "adduct ion property", "Physical measurable characteristic of an adduct ion.", false},
3037
+    {MS_scan_number, "MS:1003057", "scan number", "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run.", false},
3038
+    {MS_spectrum_property, "MS:1003058", "spectrum property", "Inherent or measurable characteristic of a spectrum.", false},
3039
+    {MS_number_of_peaks, "MS:1003059", "number of peaks", "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points.", false},
3040
+    {MS_number_of_data_points, "MS:1003060", "number of data points", "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks.", false},
3041
+    {MS_spectrum_name, "MS:1003061", "spectrum name", "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection.", false},
3042
+    {MS_spectrum_index, "MS:1003062", "spectrum index", "Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0.", false},
3043
+    {MS_universal_spectrum_identifier, "MS:1003063", "universal spectrum identifier", "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library.", false},
3044
+    {MS_spectrum_aggregation_attribute, "MS:1003064", "spectrum aggregation attribute", "Non-inherent characteristic attributed to spectrum aggregation.", false},
3045
+    {MS_spectrum_aggregation_type, "MS:1003065", "spectrum aggregation type", "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.).", false},
3046
+    {MS_singleton_spectrum, "MS:1003066", "singleton spectrum", "Spectrum that is not the result of some aggregation process.", false},
3047
+    {MS_consensus_spectrum, "MS:1003067", "consensus spectrum", "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates.", false},
3048
+    {MS_best_replicate_spectrum, "MS:1003068", "best replicate spectrum", "Spectrum that is considered the most representative from a pool of replicate spectra.", false},
3049
+    {MS_number_of_replicate_spectra_available, "MS:1003069", "number of replicate spectra available", "Number of replicate spectra available for use during the aggregation process.", false},
3050
+    {MS_number_of_replicate_spectra_used, "MS:1003070", "number of replicate spectra used", "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm.", false},
3051
+    {MS_spectrum_origin_attribute, "MS:1003071", "spectrum origin attribute", "Non-inherent characteristic attributed to spectrum aggregation.", false},
3052
+    {MS_spectrum_origin_type, "MS:1003072", "spectrum origin type", "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.).", false},
3053
+    {MS_observed_spectrum, "MS:1003073", "observed spectrum", "Spectrum that originates from an analysis attempt of a single analyte species on an instrument.", false},
3054
+    {MS_predicted_spectrum, "MS:1003074", "predicted spectrum", "Spectrum that originates from a compututational algorithm that attempts to predict spectra.", false},
3055
+    {MS_demultiplexed_spectrum, "MS:1003075", "demultiplexed spectrum", "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species.", false},
3056
+    {MS_uninterpreted_spectrum, "MS:1003076", "uninterpreted spectrum", "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features.", false},
3057
+    {MS_interpreted_spectrum, "MS:1003077", "interpreted spectrum", "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature.", false},
3058
+    {MS_interpreted_spectrum_attribute, "MS:1003078", "interpreted spectrum attribute", "Non-inherent characteristic attributed to an interpreted spectrum.", false},
3059
+    {MS_total_unassigned_intensity_fraction, "MS:1003079", "total unassigned intensity fraction", "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum.", false},
3060
+    {MS_top_20_peak_unassigned_intensity_fraction, "MS:1003080", "top 20 peak unassigned intensity fraction", "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum.", false},
3061
+    {MS_unidentified_modification_monoisotopic_mass_delta, "MS:1003081", "unidentified modification monoisotopic mass delta", "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML.", false},
3062
+    {MS_MS_DIAL, "MS:1003082", "MS-DIAL", "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors.", false},
3063
+    {MS_raw_data_file, "MS:1003083", "raw data file", "Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file).", false},
3064
+    {MS_processed_data_file, "MS:1003084", "processed data file", "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument.", false},
3065
+    {MS_previous_MSn_1_scan_precursor_intensity, "MS:1003085", "previous MSn-1 scan precursor intensity", "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes.", false},
3066
+    {MS_precursor_apex_intensity, "MS:1003086", "precursor apex intensity", "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope.", false},
3067
+    {MS_supported_by_repository_but_incomplete_data_and_or_metadata, "MS:1003087", "supported by repository but incomplete data and/or metadata", "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available.", false},
3068
+    {MS_truncation_and_zlib_compression, "MS:1003088", "truncation and zlib compression", "Data array compression using mantissa bit truncation followed by zlib compression.", false},
3069
+    {MS_truncation__delta_prediction_and_zlib_compression, "MS:1003089", "truncation, delta prediction and zlib compression", "Data array compression using mantissa bit truncation, delta prediction and zlib compression.", false},
3070
+    {MS_truncation__linear_prediction_and_zlib_compression, "MS:1003090", "truncation, linear prediction and zlib compression", "Data array compression using mantissa bit truncation, linear prediction and zlib compression.", false},
3071
+    {MS_binary_data_compression_parameter, "MS:1003091", "binary data compression parameter", "Settable parameter for a binary data compression event.", false},
3072
+    {MS_number_of_mantissa_bits_truncated, "MS:1003092", "number of mantissa bits truncated", "Number of extraneous mantissa bits truncated to improve subsequent compression.", false},
3073
+    {MS_Lys_N, "MS:1003093", "Lys-N", "Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues.", false},
3074
+    {MS_Orbitrap_Exploris_240, "MS:1003094", "Orbitrap Exploris 240", "Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS.", false},
3075
+    {MS_Orbitrap_Exploris_120, "MS:1003095", "Orbitrap Exploris 120", "Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS.", false},
3076
+    {MS_LTQ_Orbitrap_Velos_Pro, "MS:1003096", "LTQ Orbitrap Velos Pro", "Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro.", false},
3077
+    {MS_MaxQuant_protein_group_level_score, "MS:1003097", "MaxQuant protein group-level score", "The probability based MaxQuant protein group score.", false},
3078
+    {MS_Andromeda_peptide_PEP, "MS:1003098", "Andromeda peptide PEP", "Peptide probability from Andromeda.", false},
3079
+    {MS_MaxQuant_DIA_peptide_PEP, "MS:1003099", "MaxQuant-DIA peptide PEP", "Peptide probability from MaxQuant-DIA algorithm.", false},
3080
+    {MS_MaxQuant_DIA_score, "MS:1003100", "MaxQuant-DIA score", "PSM evidence score from MaxQuant-DIA algorithm.", false},
3081
+    {MS_MaxQuant_DIA_PEP, "MS:1003101", "MaxQuant-DIA PEP", "PSM evidence PEP probability from MaxQuant-DIA algorithm.", false},
3082
+    {MS_NIST_msp_comment, "MS:1003102", "NIST msp comment", "Term for a comment field withing the NIST msp file format", false},
3083
+    {MS_ion_interpretation_format, "MS:1003103", "ion interpretation format", "Interpretation format used for annotating individual spectrum ion peaks.", false},
3084
+    {MS_peptide_ion_interpretation_format, "MS:1003104", "peptide ion interpretation format", "Interpretation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions.", false},
3085
+    {MS_cross_linked_peptide_ion_interpretation_format, "MS:1003105", "cross-linked peptide ion interpretation format", "Interpretation format designed specifically for cross-linked peptide ion peaks.", false},
3086
+    {MS_glycan_ion_interpretation_format, "MS:1003106", "glycan ion interpretation format", "Interpretation format designed specifically for glycan ion peaks.", false},
3087
+    {MS_lipid_ion_interpretation_format, "MS:1003107", "lipid ion interpretation format", "Interpretation format designed specifically for lipid ion peaks.", false},
3088
+    {MS_PatternLab, "MS:1003108", "PatternLab", "PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data.", false},
3089
+    {MS_SIM_XL, "MS:1003109", "SIM-XL", "Identifying cross-linked peptides in complex protein mixtures", false},
3090
+    {MS_SIM_XL_score, "MS:1003110", "SIM-XL score", "SIM-XL identification search engine score", false},
3091
+    {MS_QUIN_XL, "MS:1003111", "QUIN-XL", "Quantification of cross-linked peptides in complex protein mixtures", false},
3092
+    {MS_Orbitrap_ID_X, "MS:1003112", "Orbitrap ID-X", "Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.", false},
3011 3093
     {UNIMOD_unimod_root_node, "UNIMOD:0", "unimod root node", "The root node of the unimod modifications ontology.", false},
3012 3094
     {UNIMOD_Acetyl, "UNIMOD:1", "Acetyl", "Acetylation.", false},
3013 3095
     {UNIMOD_Amidated, "UNIMOD:2", "Amidated", "Amidation.", false},
... ...
@@ -3920,7 +4002,7 @@ const TermInfo termInfos_[] =
3920 4002
     {UNIMOD_GGQ, "UNIMOD:1292", "GGQ", "SUMOylation leaving GlyGlyGln.", false},
3921 4003
     {UNIMOD_QTGG, "UNIMOD:1293", "QTGG", "SUMOylation leaving GlnThrGlyGly.", false},
3922 4004
     {UNIMOD_Label_13C_3_, "UNIMOD:1296", "Label:13C(3)", "13C3 label for SILAC.", false},
3923
-    {UNIMOD_Label_13C_3_15N_1_, "UNIMOD:1297", "Label:13C(3)15N(1)", "13C3 15N1 label for SILAC.", false},
4005
+    {UNIMOD_Label_13C_3_15N_1_, "UNIMOD:1297", "Label:13C(3)15N(1)", "SILAC or AQUA label.", false},
3924 4006
     {UNIMOD_Label_13C_4_15N_1_, "UNIMOD:1298", "Label:13C(4)15N(1)", "13C4 15N1 label for SILAC.", false},
3925 4007
     {UNIMOD_Label_2H_10_, "UNIMOD:1299", "Label:2H(10)", "2H(10) label.", false},
3926 4008
     {UNIMOD_Label_2H_4_13C_1_, "UNIMOD:1300", "Label:2H(4)13C(1)", "Label:2H(4)13C(1).", false},
... ...
@@ -3975,7 +4057,7 @@ const TermInfo termInfos_[] =
3975 4057
     {UNIMOD_phenylsulfonylethyl, "UNIMOD:1382", "phenylsulfonylethyl", "Reaction with phenyl vinyl sulfone.", false},
3976 4058
     {UNIMOD_PyridoxalPhosphateH2, "UNIMOD:1383", "PyridoxalPhosphateH2", "PLP bound to lysine reduced by sodium borohydride (NaBH4) to create amine linkage.", false},
3977 4059
     {UNIMOD_Homocysteic_acid, "UNIMOD:1384", "Homocysteic_acid", "Methionine oxidation to homocysteic acid.", false},
3978
-    {UNIMOD_Hydroxamic_acid, "UNIMOD:1385", "Hydroxamic_acid", "Conversion of carboxylic acid to hydroxamic acid.", false},
4060
+    {UNIMOD_Hydroxamic_acid, "UNIMOD:1385", "Hydroxamic_acid", "ADP-ribosylation followed by conversion to hydroxamic acid via hydroxylamine.", false},
3979 4061
     {UNIMOD_3_phosphoglyceryl, "UNIMOD:1387", "3-phosphoglyceryl", "3-phosphoglyceryl.", false},
3980 4062
     {UNIMOD_HN2_mustard, "UNIMOD:1388", "HN2_mustard", "Modification by hydroxylated mechloroethamine (HN-2).", false},
3981 4063
     {UNIMOD_HN3_mustard, "UNIMOD:1389", "HN3_mustard", "Modification by hydroxylated tris-(2-chloroethyl)amine (HN-3).", false},
... ...
@@ -4495,6 +4577,9 @@ const TermInfo termInfos_[] =
4495 4577
     {UNIMOD_shTMT, "UNIMOD:2015", "shTMT", "Super Heavy Tandem Mass Tag.", false},
4496 4578
     {UNIMOD_TMTpro, "UNIMOD:2016", "TMTpro", "TMTpro 16plex Tandem Mass Tag.", false},
4497 4579
     {UNIMOD_TMTpro_zero, "UNIMOD:2017", "TMTpro_zero", "Native TMTpro Tandem Mass Tag.", false},
4580
+    {UNIMOD_Kdo, "UNIMOD:2022", "Kdo", "Glycosylation with KDO.", false},
4581
+    {UNIMOD_Andro_H2O, "UNIMOD:2025", "Andro-H2O", "Andrographolide with the loss of H2O.", false},
4582
+    {UNIMOD_His_O_2_, "UNIMOD:2027", "His+O(2)", "Photo-induced histidine adduct.", false},
4498 4583
     {UO_unit, "UO:0000000", "unit", "A unit of measurement is a standardized quantity of a physical quality.", false},
4499 4584
     {UO_length_unit, "UO:0000001", "length unit", "A unit which is a standard measure of the distance between two points.", false},
4500 4585
     {UO_mass_unit, "UO:0000002", "mass unit", "A unit which is a standard measure of the amount of matter/energy of a physical object.", false},
... ...
@@ -4534,7 +4619,7 @@ const TermInfo termInfos_[] =
4534 4619
     {UO_year, "UO:0000036", "year", "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.", false},
4535 4620
     {UO_milliampere, "UO:0000037", "milliampere", "An electric current unit current which is equal to one thousandth of an ampere or 10^[-3] A.", false},
4536 4621
     {UO_microampere, "UO:0000038", "microampere", "An electric current unit current which is equal to one millionth of an ampere or 10^[-6] A.", false},
4537
-    {UO_micromole, "UO:0000039", "micromole", "A substance unit equal to a millionth of a mol or 10^[-6] mol.", false},
4622
+    {UO_micromole_300000039, "UO:0000039", "micromole (UO:300000039)", "A substance unit equal to a millionth of a mol or 10^[-6] mol.", false},
4538 4623
     {UO_millimole, "UO:0000040", "millimole", "A substance unit equal to a thousandth of a mol or 10^[-3] mol.", false},
4539 4624
     {UO_nanomole, "UO:0000041", "nanomole", "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.", false},
4540 4625
     {UO_picomole, "UO:0000042", "picomole", "A substance unit equal to 10^[-12] mol.", false},
... ...
@@ -4873,6 +4958,8 @@ const TermInfo termInfos_[] =
4873 4958
     {UO_metric_cup, "UO:0010045", "metric cup", "A metric cup is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 250mL volume.", false},
4874 4959
     {UO_united_states_customary_cup, "UO:0010046", "united states customary cup", "A United States customary units cup is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 236.59 mL volume.", false},
4875 4960
     {UO_united_states_fda_cup, "UO:0010047", "united states fda cup", "A United States FDA cup is a unit of measurement of volume used by the US Federal Department of Agriculture as a nutritional serving measure. It equals a 240 mL volume.", false},
4961
+    {UO_micromole_300010048, "UO:0010048", "micromole (UO:300010048)", "A substance unit which is equal to one millionth of a mole.", false},
4962
+    {UO_gram_per_square_meter, "UO:0010049", "gram per square meter", "An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared.", false},
4876 4963
 }; // termInfos_
4877 4964
 
4878 4965
 
... ...
@@ -4965,6 +5052,7 @@ CVIDPair relationsIsA_[] =
4965 5052
     {MS_charge_deconvolution, MS_data_processing_action},
4966 5053
     {MS_peak_picking, MS_data_processing_action},
4967 5054
     {MS_charge_state, MS_ion_selection_attribute},
5055
+    {MS_charge_state, MS_ion_property},
4968 5056
     {MS_peak_intensity, MS_ion_selection_attribute},
4969 5057
     {MS_collision_energy, MS_precursor_activation_attribute},
4970 5058
     {MS_emulsion, MS_sample_state},
... ...
@@ -5114,6 +5202,7 @@ CVIDPair relationsIsA_[] =
5114 5202
     {MS_base_peak, MS_peak},
5115 5203
     {MS_field_free_region, MS_ion_optics_attribute},
5116 5204
     {MS_magnetic_deflection, MS_ion_optics_type},
5205
+    {MS_molecular_mass, MS_molecular_entity_property},
5117 5206
     {MS_multiphoton_ionization, MS_ionization_type},
5118 5207
     {MS_total_ion_current_chromatogram, MS_ion_current_chromatogram},
5119 5208
     {MS_transmission, MS_instrument_attribute},
... ...
@@ -5145,7 +5234,7 @@ CVIDPair relationsIsA_[] =
5145 5234
     {MS_selected_ion_flow_tube, MS_ion_optics_type},
5146 5235
     {MS_sustained_off_resonance_irradiation, MS_dissociation_method},
5147 5236
     {MS_stored_waveform_inverse_fourier_transform, MS_mass_analyzer_type},
5148
-    {MS_total_ion_current, MS_spectrum_attribute},
5237
+    {MS_total_ion_current, MS_spectrum_property},
5149 5238
     {MS_time_lag_focusing, MS_ion_optics_type},
5150 5239
     {MS_cyclotron, MS_mass_analyzer_type},
5151 5240
     {MS_linear_ion_trap, MS_ion_trap},
... ...
@@ -5174,7 +5263,7 @@ CVIDPair relationsIsA_[] =
5174 5263
     {MS_ion_to_photon_detector, MS_detector_type},
5175 5264
     {MS_point_collector, MS_detector_type},
5176 5265
     {MS_postacceleration_detector, MS_detector_type},
5177
-    {MS_adduct_ion, MS_ion},
5266
+    {MS_adduct_ion, MS_adduct},
5178 5267
     {MS_adiabatic_ionization, MS_ionization_type},
5179 5268
     {MS_associative_ionization, MS_ionization_type},
5180 5269
     {MS_atmospheric_pressure_photoionization, MS_atmospheric_pressure_ionization},
... ...
@@ -5237,14 +5326,13 @@ CVIDPair relationsIsA_[] =
5237 5326
     {MS_Thermo_Scientific_instrument_model, MS_Thermo_Fisher_Scientific_instrument_model},
5238 5327
     {MS_Applied_Biosystems_instrument_model, MS_instrument_model},
5239 5328
     {MS_instrument_attribute, MS_object_attribute},
5240
-    {MS_zoom_scan, MS_spectrum_attribute},
5241
-    {MS_spectrum_attribute, MS_object_attribute},
5329
+    {MS_zoom_scan, MS_scan_attribute},
5242 5330
     {MS_scan_window_upper_limit, MS_selection_window_attribute},
5243 5331
     {MS_scan_window_lower_limit, MS_selection_window_attribute},
5244 5332
     {MS_dwell_time, MS_scan_attribute},
5245 5333
     {MS_scan_attribute, MS_object_attribute},
5246
-    {MS_base_peak_m_z, MS_spectrum_attribute},
5247
-    {MS_base_peak_intensity, MS_spectrum_attribute},
5334
+    {MS_base_peak_m_z, MS_spectrum_property},
5335
+    {MS_base_peak_intensity, MS_spectrum_property},
5248 5336
     {MS_activation_energy, MS_precursor_activation_attribute},
5249 5337
     {MS_ms_level, MS_spectrum_attribute},
5250 5338
     {MS_filter_string, MS_scan_attribute},
... ...
@@ -5258,10 +5346,10 @@ CVIDPair relationsIsA_[] =
5258 5346
     {MS_64_bit_integer, MS_binary_data_type},
5259 5347
     {MS_64_bit_float, MS_binary_data_type},
5260 5348
     {MS_Waters_raw_format, MS_mass_spectrometer_file_format},
5261
-    {MS_highest_observed_m_z, MS_spectrum_attribute},
5262 5349
     {MS_highest_observed_m_z, MS_chromatogram_attribute},
5263
-    {MS_lowest_observed_m_z, MS_spectrum_attribute},
5350
+    {MS_highest_observed_m_z, MS_spectrum_property},
5264 5351
     {MS_lowest_observed_m_z, MS_chromatogram_attribute},
5352
+    {MS_lowest_observed_m_z, MS_spectrum_property},
5265 5353
     {MS_instrument_serial_number, MS_instrument_attribute},
5266 5354
     {MS_file_format_conversion, MS_data_transformation},
5267 5355
     {MS_Xcalibur, MS_Thermo_Finnigan_software},
... ...
@@ -5325,6 +5413,7 @@ CVIDPair relationsIsA_[] =
5325 5413
     {MS_zlib_compression, MS_binary_data_compression_type},
5326 5414
     {MS_mean_of_spectra, MS_spectra_combination},
5327 5415
     {MS_no_compression, MS_binary_data_compression_type},
5416
+    {MS_source_data_file, MS_spectrum_attribute},
5328 5417
     {MS_LCQ_Fleet, MS_Thermo_Finnigan_instrument_model},
5329 5418
     {MS_MS1_spectrum, MS_mass_spectrum},
5330 5419
     {MS_MSn_spectrum, MS_mass_spectrum},
... ...
@@ -5368,9 +5457,9 @@ CVIDPair relationsIsA_[] =
5368 5457
     {MS_ProteoWizard_software, MS_data_processing_software},
5369 5458
     {MS_preset_scan_configuration, MS_scan_attribute},
5370 5459
     {MS_wavelength_array, MS_binary_data_array},
5371
-    {MS_highest_observed_wavelength, MS_spectrum_attribute},
5460
+    {MS_highest_observed_wavelength, MS_spectrum_property},
5372 5461
     {MS_highest_observed_wavelength, MS_chromatogram_attribute},
5373
-    {MS_lowest_observed_wavelength, MS_spectrum_attribute},
5462
+    {MS_lowest_observed_wavelength, MS_spectrum_property},
5374 5463
     {MS_lowest_observed_wavelength, MS_chromatogram_attribute},
5375 5464
     {MS_PDA_spectrum_OBSOLETE, MS_data_file_content},
5376 5465
     {MS_PDA_spectrum_OBSOLETE, MS_spectrum_type},
... ...
@@ -5628,12 +5717,12 @@ CVIDPair relationsIsA_[] =
5628 5717
     {MS_isolation_window_upper_limit_OBSOLETE, MS_isolation_window_attribute},
5629 5718
     {MS_isolation_window_lower_limit_OBSOLETE, MS_isolation_window_attribute},
5630 5719
     {MS_no_combination, MS_spectra_combination},
5631
-    {MS_spectrum_title, MS_spectrum_attribute},
5632 5720
     {MS_spectrum_title, MS_spectrum_identification_result_details},
5633
-    {MS_peak_list_scans, MS_spectrum_attribute},
5721
+    {MS_spectrum_title, MS_spectrum_attribute},
5634 5722
     {MS_peak_list_scans, MS_spectrum_identification_result_details},
5635
-    {MS_peak_list_raw_scans, MS_spectrum_attribute},
5723
+    {MS_peak_list_scans, MS_spectrum_property},
5636 5724
     {MS_peak_list_raw_scans, MS_spectrum_identification_result_details},
5725
+    {MS_peak_list_raw_scans, MS_spectrum_property},
5637 5726
     {MS_custom_unreleased_software_tool, MS_software},
5638 5727
     {MS_mass_resolving_power, MS_scan_attribute},
5639 5728
     {MS_area_peak_picking, MS_peak_picking},
... ...
@@ -5695,13 +5784,15 @@ CVIDPair relationsIsA_[] =
5695 5784
     {MS_LTQ_Velos_ETD, MS_Thermo_Scientific_instrument_model},
5696 5785
     {MS_run_attribute, MS_object_attribute},
5697 5786
     {MS_fraction_identifier, MS_run_attribute},
5698
-    {MS_peptide, MS_chemical_compound},
5699
-    {MS_isoelectric_point, MS_chemical_compound_attribute},
5787
+    {MS_molecule, MS_molecular_entity},
5788
+    {MS_peptide, MS_molecule},
5789
+    {MS_isoelectric_point, MS_molecular_entity_property},
5700 5790
     {MS_predicted_isoelectric_point, MS_isoelectric_point},
5701
-    {MS_empirical_formula, MS_chemical_compound_formula},
5702
-    {MS_molecular_formula, MS_chemical_compound_formula},
5703
-    {MS_structural_formula, MS_chemical_compound_formula},
5704
-    {MS_SMILES_string, MS_chemical_compound_formula},
5791
+    {MS_chemical_formula, MS_molecular_entity_attribute},
5792
+    {MS_empirical_formula, MS_chemical_formula},
5793
+    {MS_molecular_formula, MS_chemical_formula},
5794
+    {MS_structural_formula, MS_chemical_formula},
5795
+    {MS_SMILES_formula, MS_chemical_formula},
5705 5796
     {MS_collision_gas_pressure, MS_precursor_activation_attribute},
5706 5797
     {MS_4000_QTRAP_OBSOLETE, MS_SCIEX_instrument_model},
5707 5798
     {MS_SRM_software, MS_software},
... ...
@@ -5714,18 +5805,19 @@ CVIDPair relationsIsA_[] =
5714 5805
     {MS_external_reference_identifier, MS_external_reference_data},
5715 5806
     {MS_PubMed_identifier, MS_external_reference_identifier},
5716 5807
     {MS_interchannel_delay, MS_scan_attribute},
5717
-    {MS_protein, MS_chemical_compound},
5808
+    {MS_protein, MS_molecule},
5718 5809
     {MS_protein_short_name, MS_protein_attribute},
5719 5810
     {MS_protein_attribute, MS_quantification_object_attribute},
5720 5811
     {MS_protein_accession, MS_protein_attribute},
5812
+    {MS_protein_accession, MS_peptide_to_protein_mapping_attribute},
5721 5813
     {MS_protein_name, MS_protein_attribute},
5722
-    {MS_unmodified_peptide_sequence, MS_peptide_attribute},
5723
-    {MS_modified_peptide_sequence, MS_peptide_attribute},
5724
-    {MS_peptide_labeling_state, MS_peptide_attribute},
5725
-    {MS_heavy_labeled_peptide, MS_peptide_labeling_state},
5726
-    {MS_unlabeled_peptide, MS_peptide_labeling_state},
5727
-    {MS_peptide_group_label, MS_peptide_attribute},
5728
-    {MS_retention_time, MS_peptide_attribute},
5814
+    {MS_stripped_peptide_sequence, MS_peptidoform_attribute},
5815
+    {MS_peptidoform_sequence, MS_peptidoform_attribute},
5816
+    {MS_peptidoform_labeling_state, MS_peptidoform_attribute},
5817
+    {MS_heavy_labeled_peptidoform, MS_peptidoform_labeling_state},
5818
+    {MS_unlabeled_peptidoform, MS_peptidoform_labeling_state},
5819
+    {MS_peptidoform_group_label, MS_peptidoform_attribute},
5820
+    {MS_retention_time, MS_peptidoform_attribute},
5729 5821
     {MS_local_retention_time, MS_retention_time},
5730 5822
     {MS_normalized_retention_time, MS_retention_time},
5731 5823
     {MS_predicted_retention_time, MS_retention_time},
... ...
@@ -5856,7 +5948,9 @@ CVIDPair relationsIsA_[] =
5856 5948
     {MS_SEQUEST_CullTo, MS_SEQUEST_ProcessCV},
5857 5949
     {MS_SEQUEST_modeCV, MS_SEQUEST_input_parameter},
5858 5950
     {MS_SEQUEST_Full, MS_SEQUEST_modeCV},
5951
+    {MS_n_terminal_flanking_residue, MS_peptide_to_protein_mapping_attribute},
5859 5952
     {MS_n_terminal_flanking_residue, MS_peptide_sequence_level_identification_attribute},
5953
+    {MS_c_terminal_flanking_residue, MS_peptide_to_protein_mapping_attribute},
5860 5954
     {MS_c_terminal_flanking_residue, MS_peptide_sequence_level_identification_attribute},
5861 5955
     {MS_retention_time_s__OBSOLETE, MS_peptide_sequence_level_identification_attribute},
5862 5956
     {MS_single_protein_identification_statistic, MS_protein_level_identification_attribute},
... ...
@@ -7551,11 +7645,11 @@ CVIDPair relationsIsA_[] =
7551 7645
     {MS_7000B_Triple_Quadrupole_GC_MS, MS_Agilent_instrument_model},
7552 7646
     {MS_7800_Quadrupole_ICP_MS, MS_Agilent_instrument_model},
7553 7647
     {MS_8800_Triple_Quadrupole_ICP_MS, MS_Agilent_instrument_model},
7648
+    {MS_ion, MS_molecular_entity},
7554 7649
     {MS_positive_mode_adduct_ion, MS_adduct_ion},
7555 7650
     {MS_negative_mode_adduct_ion, MS_adduct_ion},
7556
-    {MS_adduct_ion_attribute, MS_object_attribute},
7557
-    {MS_adduct_ion_mass, MS_adduct_ion_attribute},
7558
-    {MS_adduct_ion_isotope, MS_adduct_ion_attribute},
7651
+    {MS_adduct_ion_X_m_z, MS_adduct_ion_property},
7652
+    {MS_adduct_ion_isotope, MS_adduct_ion_property},
7559 7653
     {MS_Regular_expression_for_adduct_ion_formula, MS_regular_expression},
7560 7654
     {MS_adduct_ion_formula, MS_adduct_ion_attribute},
7561 7655
     {MS_inverse_reduced_ion_mobility, MS_ion_selection_attribute},
... ...
@@ -7709,11 +7803,12 @@ CVIDPair relationsIsA_[] =
7709 7803
     {MS_TopMG_proteoform_level_FDR, MS_search_engine_specific_score_for_proteoforms},
7710 7804
     {MS_TopMG_spectral_p_value, MS_PSM_level_p_value},
7711 7805
     {MS_TopMG_spectral_p_value, MS_PSM_level_search_engine_specific_statistic},
7712
-    {MS_collisional_cross_sectional_area, MS_chemical_compound_attribute},
7806
+    {MS_collisional_cross_sectional_area, MS_molecular_entity_property},
7713 7807
     {MS_hr_ms_compound_identification_confidence_level, MS_small_molecule_identification_attribute},
7714 7808
     {MS_isotopic_ion_MS_peak, MS_peak},
7715 7809
     {MS_isotopomer_MS_peak, MS_isotopic_ion_MS_peak},
7716 7810
     {MS_isotopologue_MS_peak, MS_isotopic_ion_MS_peak},
7811
+    {MS_isomer, MS_molecule},
7717 7812
     {MS_isotopomer, MS_isomer},
7718 7813
     {MS_isotopologue, MS_isomer},
7719 7814
     {MS_mean, MS_study_variable_average_function},
... ...
@@ -7802,6 +7897,85 @@ CVIDPair relationsIsA_[] =
7802 7897
     {MS_Orbitrap_Exploris_480, MS_Thermo_Scientific_instrument_model},
7803 7898
     {MS_Orbitrap_Eclipse, MS_Thermo_Scientific_instrument_model},
7804 7899
     {MS_Mascot_MinNumSigUniqueSeqs, MS_Mascot_input_parameter},
7900
+    {MS_CPTAC_accession_number, MS_external_reference_identifier},
7901
+    {MS_compound_identification_confidence_code_in_MS_DIAL, MS_small_molecule_identification_attribute},
7902
+    {MS_atom, MS_molecular_entity},
7903
+    {MS_small_molecule, MS_molecule},
7904
+    {MS_metabolite, MS_small_molecule},
7905
+    {MS_ribonucleotide, MS_small_molecule},
7906
+    {MS_deoxyribonucleotide, MS_small_molecule},
7907
+    {MS_amino_acid, MS_small_molecule},
7908
+    {MS_monosaccharide, MS_small_molecule},
7909
+    {MS_nucleic_acid, MS_molecule},
7910
+    {MS_polysaccharide, MS_molecule},
7911
+    {MS_number_of_residues, MS_peptide_attribute},
7912
+    {MS_number_of_missed_cleavages, MS_peptide_attribute},
7913
+    {MS_peptide_to_protein_mapping, MS_peptide_attribute},
7914
+    {MS_peptide_to_protein_mapping_attribute, MS_peptide_to_protein_mapping},
7915
+    {MS_protein_sequence_offset, MS_peptide_to_protein_mapping_attribute},
7916
+    {MS_number_of_enzymatic_termini, MS_peptide_to_protein_mapping_attribute},
7917
+    {MS_peptidoform, MS_peptide},
7918
+    {MS_peptidoform_ion, MS_peptidoform},
7919
+    {MS_theoretical_monoisotopic_m_z, MS_peptidoform_ion_property},
7920
+    {MS_theoretical_average_m_z, MS_peptidoform_ion_property},
7921
+    {MS_adduct, MS_molecule},
7922
+    {MS_scan_number, MS_scan_attribute},
7923
+    {MS_number_of_peaks, MS_spectrum_property},
7924
+    {MS_number_of_data_points, MS_spectrum_property},
7925
+    {MS_spectrum_name, MS_spectrum_attribute},
7926
+    {MS_spectrum_index, MS_spectrum_attribute},
7927
+    {MS_universal_spectrum_identifier, MS_spectrum_attribute},
7928
+    {MS_spectrum_aggregation_attribute, MS_spectrum_attribute},
7929
+    {MS_spectrum_aggregation_type, MS_spectrum_aggregation_attribute},
7930
+    {MS_singleton_spectrum, MS_spectrum_aggregation_type},
7931
+    {MS_consensus_spectrum, MS_spectrum_aggregation_type},
7932
+    {MS_best_replicate_spectrum, MS_spectrum_aggregation_type},
7933
+    {MS_number_of_replicate_spectra_available, MS_spectrum_aggregation_attribute},
7934
+    {MS_number_of_replicate_spectra_used, MS_spectrum_aggregation_attribute},
7935
+    {MS_spectrum_origin_attribute, MS_spectrum_attribute},
7936
+    {MS_spectrum_origin_type, MS_spectrum_origin_attribute},
7937
+    {MS_observed_spectrum, MS_spectrum_origin_type},
7938
+    {MS_predicted_spectrum, MS_spectrum_origin_type},
7939
+    {MS_demultiplexed_spectrum, MS_spectrum_origin_type},
7940
+    {MS_uninterpreted_spectrum, MS_spectrum},
7941
+    {MS_interpreted_spectrum, MS_spectrum},
7942
+    {MS_total_unassigned_intensity_fraction, MS_interpreted_spectrum_attribute},
7943
+    {MS_top_20_peak_unassigned_intensity_fraction, MS_interpreted_spectrum_attribute},
7944
+    {MS_unidentified_modification_monoisotopic_mass_delta, MS_peptide_modification_details},
7945
+    {MS_MS_DIAL, MS_small_molecule_analysis_software},
7946
+    {MS_MS_DIAL, MS_data_processing_software},
7947
+    {MS_raw_data_file, MS_source_data_file},
7948
+    {MS_processed_data_file, MS_source_data_file},
7949
+    {MS_previous_MSn_1_scan_precursor_intensity, MS_intensity_of_precursor_ion},
7950
+    {MS_previous_MSn_1_scan_precursor_intensity, MS_spectrum_attribute},
7951
+    {MS_precursor_apex_intensity, MS_intensity_of_precursor_ion},
7952
+    {MS_precursor_apex_intensity, MS_spectrum_attribute},
7953
+    {MS_supported_by_repository_but_incomplete_data_and_or_metadata, MS_Experiment_additional_parameter},
7954
+    {MS_truncation_and_zlib_compression, MS_binary_data_compression_type},
7955
+    {MS_truncation__delta_prediction_and_zlib_compression, MS_binary_data_compression_type},
7956
+    {MS_truncation__linear_prediction_and_zlib_compression, MS_binary_data_compression_type},
7957
+    {MS_number_of_mantissa_bits_truncated, MS_binary_data_compression_parameter},
7958
+    {MS_Lys_N, MS_cleavage_agent_name},
7959
+    {MS_Orbitrap_Exploris_240, MS_Thermo_Scientific_instrument_model},
7960
+    {MS_Orbitrap_Exploris_120, MS_Thermo_Scientific_instrument_model},
7961
+    {MS_LTQ_Orbitrap_Velos_Pro, MS_Thermo_Scientific_instrument_model},
7962
+    {MS_MaxQuant_protein_group_level_score, MS_search_engine_specific_score_for_protein_groups},
7963
+    {MS_Andromeda_peptide_PEP, MS_search_engine_specific_peptide_sequence_level_identification_statistic},
7964
+    {MS_MaxQuant_DIA_peptide_PEP, MS_search_engine_specific_peptide_sequence_level_identification_statistic},
7965
+    {MS_MaxQuant_DIA_score, MS_PSM_level_search_engine_specific_statistic},
7966
+    {MS_MaxQuant_DIA_PEP, MS_PSM_level_search_engine_specific_statistic},
7967
+    {MS_NIST_msp_comment, MS_spectrum_attribute},
7968
+    {MS_ion_interpretation_format, MS_interpreted_spectrum_attribute},
7969
+    {MS_peptide_ion_interpretation_format, MS_ion_interpretation_format},
7970
+    {MS_cross_linked_peptide_ion_interpretation_format, MS_ion_interpretation_format},
7971
+    {MS_glycan_ion_interpretation_format, MS_ion_interpretation_format},
7972
+    {MS_lipid_ion_interpretation_format, MS_ion_interpretation_format},
7973
+    {MS_PatternLab, MS_quantitation_software_name},
7974
+    {MS_PatternLab, MS_analysis_software},
7975
+    {MS_SIM_XL, MS_analysis_software},
7976
+    {MS_SIM_XL_score, MS_PSM_level_search_engine_specific_statistic},
7977
+    {MS_QUIN_XL, MS_quantitation_software_name},
7978
+    {MS_Orbitrap_ID_X, MS_Thermo_Scientific_instrument_model},
7805 7979
     {UNIMOD_Acetyl, UNIMOD_unimod_root_node},
7806 7980
     {UNIMOD_Amidated, UNIMOD_unimod_root_node},
7807 7981
     {UNIMOD_Biotin, UNIMOD_unimod_root_node},
... ...
@@ -9288,6 +9462,9 @@ CVIDPair relationsIsA_[] =
9288 9462
     {UNIMOD_shTMT, UNIMOD_unimod_root_node},
9289 9463
     {UNIMOD_TMTpro, UNIMOD_unimod_root_node},
9290 9464
     {UNIMOD_TMTpro_zero, UNIMOD_unimod_root_node},
9465
+    {UNIMOD_Kdo, UNIMOD_unimod_root_node},
9466
+    {UNIMOD_Andro_H2O, UNIMOD_unimod_root_node},
9467
+    {UNIMOD_His_O_2_, UNIMOD_unimod_root_node},
9291 9468
     {UO_length_unit, UO_unit},
9292 9469
     {UO_mass_unit, UO_unit},
9293 9470
     {UO_time_unit, UO_unit},
... ...
@@ -9333,7 +9510,7 @@ CVIDPair relationsIsA_[] =
9333 9510
     {UO_year, UO_time_unit},
9334 9511
     {UO_milliampere, UO_electric_current_unit},
9335 9512
     {UO_microampere, UO_electric_current_unit},
9336
-    {UO_micromole, UO_substance_unit},
9513
+    {UO_micromole_300000039, UO_substance_unit},
9337 9514
     {UO_millimole, UO_substance_unit},
9338 9515
     {UO_nanomole, UO_substance_unit},
9339 9516
     {UO_picomole, UO_substance_unit},
... ...
@@ -9684,6 +9861,8 @@ CVIDPair relationsIsA_[] =
9684 9861
     {UO_metric_cup, UO_volume_unit},
9685 9862
     {UO_united_states_customary_cup, UO_volume_unit},
9686 9863
     {UO_united_states_fda_cup, UO_volume_unit},
9864
+    {UO_micromole_300010048, UO_substance_unit},
9865
+    {UO_gram_per_square_meter, UO_area_density_unit},
9687 9866
 }; // relationsIsA_
9688 9867
 
9689 9868
 
... ...
@@ -9722,29 +9901,30 @@ CVIDPair relationsPartOf_[] =
9722 9901
     {MS_instrument_attribute, MS_instrument},
9723 9902
     {MS_spectrum_attribute, MS_spectrum},
9724 9903
     {MS_scan_attribute, MS_scan},
9904
+    {MS_ion_property, MS_ion},
9725 9905
     {MS_precursor_activation_attribute, MS_precursor_activation},
9726 9906
     {MS_binary_data_array, MS_spectrum},
9727 9907
     {MS_binary_data_array, MS_chromatogram},
9728 9908
     {MS_binary_data_type, MS_spectrum},
9729 9909
     {MS_binary_data_type, MS_chromatogram},
9730
-    {MS_data_file_content, MS_raw_data_file},
9910
+    {MS_data_file_content, MS_source_data_file},
9731 9911
     {MS_spectrum_representation, MS_spectrum},
9732 9912
     {MS_software, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9733 9913
     {MS_object_attribute, MS_spectrum_generation_information},
9734 9914
     {MS_sample_attribute, MS_sample},
9735 9915
     {MS_selection_window_attribute, MS_scan},
9736 9916
     {MS_spectrum_type, MS_spectrum},
9737
-    {MS_data_file_checksum_type, MS_raw_data_file},
9917
+    {MS_data_file_checksum_type, MS_source_data_file},
9738 9918
     {MS_spectra_combination, MS_spectrum},
9739 9919
     {MS_binary_data_compression_type, MS_spectrum},
9740 9920
     {MS_binary_data_compression_type, MS_chromatogram},
9741
-    {MS_raw_data_file, MS_spectrum_generation_information},
9921
+    {MS_source_data_file, MS_spectrum_generation_information},
9742 9922
     {MS_contact_attribute, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9743 9923
     {MS_measurement_method, MS_spectrum_generation_information},
9744 9924
     {MS_chromatogram, MS_spectrum_generation_information},
9745 9925
     {MS_chromatogram_type, MS_chromatogram},
9746 9926
     {MS_data_processing_parameter, MS_spectrum_generation_information},
9747
-    {MS_native_spectrum_identifier_format, MS_raw_data_file},
9927
+    {MS_native_spectrum_identifier_format, MS_source_data_file},
9748 9928
     {MS_isolation_window_attribute, MS_scan},
9749 9929
     {MS_chromatogram_attribute, MS_chromatogram},
9750 9930
     {MS_sample_preparation, MS_sample_attribute},
... ...
@@ -9753,10 +9933,8 @@ CVIDPair relationsPartOf_[] =
9753 9933
     {MS_laser, MS_source_attribute},
9754 9934
     {MS_laser_attribute, MS_laser},
9755 9935
     {MS_laser_type, MS_laser},
9756
-    {MS_molecule, MS_chemical_compound},
9757
-    {MS_chemical_compound_attribute, MS_chemical_compound},
9758
-    {MS_chemical_compound_formula, MS_chemical_compound},
9759
-    {MS_chemical_compound, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9936
+    {MS_molecular_entity_property, MS_molecular_entity},
9937
+    {MS_molecular_entity, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9760 9938
     {MS_protein_attribute, MS_protein},
9761 9939
     {MS_peptide_attribute, MS_peptide},
9762 9940
     {MS_standard, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
... ...
@@ -9802,13 +9980,20 @@ CVIDPair relationsPartOf_[] =
9802 9980
     {MS_spectrum_identification_list_result_details, MS_spectrum_interpretation},
9803 9981
     {MS_regular_expression, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9804 9982
     {MS_special_processing, MS_spectrum_interpretation},
9805
-    {MS_native_spectrum_identifier_format__combined_spectra, MS_raw_data_file},
9983
+    {MS_native_spectrum_identifier_format__combined_spectra, MS_source_data_file},
9806 9984
     {MS_identification_parameter, MS_spectrum_interpretation},
9807 9985
     {MS_cross_linking_result_details, MS_spectrum_interpretation},
9808
-    {MS_ion, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9986
+    {MS_adduct_ion_attribute, MS_adduct_ion},
9809 9987
     {MS_external_reference_data, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9810
-    {MS_isomer, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9811 9988
     {MS_named_element, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies},
9989
+    {MS_molecular_entity_attribute, MS_molecular_entity},
9990
+    {MS_peptidoform_attribute, MS_peptidoform},
9991
+    {MS_peptidoform_ion_property, MS_peptidoform_ion},
9992
+    {MS_adduct_ion_property, MS_adduct_ion},
9993
+    {MS_spectrum_property, MS_spectrum},
9994
+    {MS_interpreted_spectrum_attribute, MS_interpreted_spectrum},
9995
+    {MS_binary_data_compression_parameter, MS_spectrum},
9996
+    {MS_binary_data_compression_parameter, MS_chromatogram},
9812 9997
 }; // relationsPartOf_
9813 9998
 
9814 9999
 
... ...
@@ -9866,7 +10051,7 @@ OtherRelationPair relationsOther_[] =
9866 10051
     {MS_exact_mass_OBSOLETE, "has_units", UO_mass_unit},
9867 10052
     {MS_ionization_energy_OBSOLETE, "has_units", UO_electronvolt},
9868 10053
     {MS_mass_defect_OBSOLETE, "has_units", UO_mass_unit},
9869
-    {MS_molecular_mass_OBSOLETE, "has_units", UO_mass_unit},
10054
+    {MS_molecular_mass, "has_units", UO_mass_unit},
9870 10055
     {MS_monoisotopic_mass_OBSOLETE, "has_units", UO_mass_unit},
9871 10056
     {MS_nominal_mass_OBSOLETE, "has_units", UO_mass_unit},
9872 10057
     {MS_accelerating_voltage, "has_units", UO_volt},
... ...
@@ -10170,6 +10355,9 @@ OtherRelationPair relationsOther_[] =
10170 10355
     {MS_ProteinProphet_peptide_group_weight, "has_domain", MS_value_between_0_and_1_inclusive},
10171 10356
     {MS_ProteinProphet_peptide_group_weight, "has_order", MS_higher_score_better},
10172 10357
     {MS_OpenPepXL_score, "has_order", MS_higher_score_better},
10358
+    {MS_unidentified_modification_monoisotopic_mass_delta, "has_units", UO_dalton},
10359
+    {MS_Lys_N, "has_regexp", MS_____K____P_},
10360
+    {MS_SIM_XL_score, "has_order", MS_higher_score_better},
10173 10361
 }; // relationsOther_
10174 10362
 
10175 10363
 
... ...
@@ -10303,7 +10491,7 @@ CVIDStringPair relationsExactSynonym_[] =
10303 10491
     {MS_Applied_Biosystems_instrument_model, "ABI"},
10304 10492
     {MS_zoom_scan, "enhanced resolution scan"},
10305 10493
     {MS_massWolf, "wolf"},
10306
-    {MS_raw_data_file, "source file"},
10494
+    {MS_source_data_file, "source file"},
10307 10495
     {MS_MS1_spectrum, "full spectrum"},
10308 10496
     {MS_MS1_spectrum, "Q1 spectrum"},
10309 10497
     {MS_MS1_spectrum, "Q3 spectrum"},
... ...
@@ -10336,7 +10524,7 @@ CVIDStringPair relationsExactSynonym_[] =
10336 10524
     {MS_electromagnetic_radiation_chromatogram, "EMR radiation chromatogram"},
10337 10525
     {MS_isoelectric_point, "pI"},
10338 10526
     {MS_predicted_isoelectric_point, "predicted pI"},
10339
-    {MS_unlabeled_peptide, "light labeled peptide"},
10527
+    {MS_unlabeled_peptidoform, "light labeled peptide"},
10340 10528
     {MS_transition, "reaction"},
10341 10529
     {MS_product_ion_m_z, "fragment ion m/z"},
10342 10530
     {MS_product_ion_intensity, "fragment ion intensity"},
... ...
@@ -10407,7 +10595,7 @@ CVIDStringPair relationsExactSynonym_[] =
10407 10595
     {UO_hour, "h"},
10408 10596
     {UO_milliampere, "mA"},
10409 10597
     {UO_microampere, "uA"},
10410
-    {UO_micromole, "umol"},
10598
+    {UO_micromole_300000039, "umol"},
10411 10599
     {UO_millimole, "mmol"},
10412 10600
     {UO_nanomole, "nmol"},
10413 10601
     {UO_picomole, "pmol"},
... ...
@@ -10739,6 +10927,9 @@ CVIDStringPair relationsExactSynonym_[] =
10739 10927
     {UO_metric_cup, "C"},
10740 10928
     {UO_united_states_customary_cup, "us customary cup"},
10741 10929
     {UO_united_states_fda_cup, "us fda cup"},
10930
+    {UO_micromole_300010048, "mmol"},
10931
+    {UO_gram_per_square_meter, "g/m^[2]"},
10932
+    {UO_gram_per_square_meter, "gram per square metre"},
10742 10933
 }; // relationsExactSynonym_
10743 10934
 
10744 10935
 
... ...
@@ -13684,6 +13875,10 @@ PropertyValuePair propertyValue_[] =
13684 13875
     {UNIMOD_Phosphoadenosine, "spec_4_hidden", "1"},
13685 13876
     {UNIMOD_Phosphoadenosine, "spec_4_position", "Anywhere"},
13686 13877
     {UNIMOD_Phosphoadenosine, "spec_4_site", "H"},
13878
+    {UNIMOD_Phosphoadenosine, "spec_5_classification", "Post-translational"},
13879
+    {UNIMOD_Phosphoadenosine, "spec_5_hidden", "1"},
13880
+    {UNIMOD_Phosphoadenosine, "spec_5_position", "Anywhere"},
13881
+    {UNIMOD_Phosphoadenosine, "spec_5_site", "S"},
13687 13882
     {UNIMOD_Hydroxycinnamyl, "approved", "1"},
13688 13883
     {UNIMOD_Hydroxycinnamyl, "delta_composition", "H(6) C(9) O(2)"},
13689 13884
     {UNIMOD_Hydroxycinnamyl, "spec_1_classification", "Post-translational"},
... ...
@@ -16638,6 +16833,10 @@ PropertyValuePair propertyValue_[] =
16638 16833
     {UNIMOD_LG_pyrrole, "spec_2_hidden", "1"},
16639 16834
     {UNIMOD_LG_pyrrole, "spec_2_position", "Any N-term"},
16640 16835
     {UNIMOD_LG_pyrrole, "spec_2_site", "N-term"},
16836
+    {UNIMOD_LG_pyrrole, "spec_3_classification", "Post-translational"},
16837
+    {UNIMOD_LG_pyrrole, "spec_3_hidden", "1"},
16838
+    {UNIMOD_LG_pyrrole, "spec_3_position", "Anywhere"},
16839
+    {UNIMOD_LG_pyrrole, "spec_3_site", "C"},
16641 16840
     {UNIMOD_LG_anhyropyrrole, "approved", "0"},
16642 16841
     {UNIMOD_LG_anhyropyrrole, "delta_composition", "H(26) C(20) O(2)"},
16643 16842
     {UNIMOD_LG_anhyropyrrole, "spec_1_classification", "Post-translational"},
... ...
@@ -18868,6 +19067,10 @@ PropertyValuePair propertyValue_[] =
18868 19067
     {UNIMOD_Label_13C_3_15N_1_, "spec_1_hidden", "1"},
18869 19068
     {UNIMOD_Label_13C_3_15N_1_, "spec_1_position", "Anywhere"},
18870 19069
     {UNIMOD_Label_13C_3_15N_1_, "spec_1_site", "A"},
19070
+    {UNIMOD_Label_13C_3_15N_1_, "spec_2_classification", "Isotopic label"},
19071
+    {UNIMOD_Label_13C_3_15N_1_, "spec_2_hidden", "1"},
19072
+    {UNIMOD_Label_13C_3_15N_1_, "spec_2_position", "Anywhere"},
19073
+    {UNIMOD_Label_13C_3_15N_1_, "spec_2_site", "S"},
18871 19074
     {UNIMOD_Label_13C_4_15N_1_, "approved", "0"},
18872 19075
     {UNIMOD_Label_13C_4_15N_1_, "delta_composition", "C(-4) 13C(4) N(-1) 15N"},
18873 19076
     {UNIMOD_Label_13C_4_15N_1_, "spec_1_classification", "Isotopic label"},
... ...
@@ -24151,23 +24354,15 @@ PropertyValuePair propertyValue_[] =
24151 24354
     {UNIMOD_Unknown_306, "spec_3_position", "Any N-term"},
24152 24355
     {UNIMOD_Unknown_306, "spec_3_site", "N-term"},
24153 24356
     {UNIMOD_Unknown_420, "approved", "0"},
24154
-    {UNIMOD_Unknown_420, "delta_composition", "H(14) C(10) N(9) O(6) S(2)"},
24357
+    {UNIMOD_Unknown_420, "delta_composition", "H(24) C(12) N(2) O(6) S(4)"},
24155 24358
     {UNIMOD_Unknown_420, "spec_1_classification", "Artefact"},
24156
-    {UNIMOD_Unknown_420, "spec_1_classification", "Artefact"},
24157
-    {UNIMOD_Unknown_420, "spec_1_hidden", "1"},
24158 24359
     {UNIMOD_Unknown_420, "spec_1_hidden", "1"},
24159
-    {UNIMOD_Unknown_420, "spec_1_position", "Anywhere"},
24160
-    {UNIMOD_Unknown_420, "spec_1_position", "Anywhere"},
24161
-    {UNIMOD_Unknown_420, "spec_1_site", "D"},
24162
-    {UNIMOD_Unknown_420, "spec_1_site", "E"},
24360
+    {UNIMOD_Unknown_420, "spec_1_position", "Any C-term"},
24361
+    {UNIMOD_Unknown_420, "spec_1_site", "C-term"},
24163 24362
     {UNIMOD_Unknown_420, "spec_2_classification", "Artefact"},
24164 24363
     {UNIMOD_Unknown_420, "spec_2_hidden", "1"},
24165
-    {UNIMOD_Unknown_420, "spec_2_position", "Any C-term"},
24166
-    {UNIMOD_Unknown_420, "spec_2_site", "C-term"},
24167
-    {UNIMOD_Unknown_420, "spec_3_classification", "Artefact"},
24168
-    {UNIMOD_Unknown_420, "spec_3_hidden", "1"},
24169
-    {UNIMOD_Unknown_420, "spec_3_position", "Any N-term"},
24170
-    {UNIMOD_Unknown_420, "spec_3_site", "N-term"},
24364
+    {UNIMOD_Unknown_420, "spec_2_position", "Any N-term"},
24365
+    {UNIMOD_Unknown_420, "spec_2_site", "N-term"},
24171 24366
     {UNIMOD_Diethylphosphothione, "approved", "0"},
24172 24367
     {UNIMOD_Diethylphosphothione, "delta_composition", "H(9) C(4) O(2) P S"},
24173 24368
     {UNIMOD_Diethylphosphothione, "spec_1_classification", "Chemical derivative"},
... ...
@@ -24444,6 +24639,28 @@ PropertyValuePair propertyValue_[] =
24444 24639
     {UNIMOD_TMTpro_zero, "spec_6_hidden", "1"},
24445 24640
     {UNIMOD_TMTpro_zero, "spec_6_position", "Anywhere"},
24446 24641
     {UNIMOD_TMTpro_zero, "spec_6_site", "T"},
24642
+    {UNIMOD_Kdo, "approved", "0"},
24643
+    {UNIMOD_Kdo, "delta_composition", "H(12) C(8) O(7)"},
24644
+    {UNIMOD_Kdo, "spec_1_classification", "O-linked glycosylation"},
24645
+    {UNIMOD_Kdo, "spec_1_classification", "O-linked glycosylation"},
24646
+    {UNIMOD_Kdo, "spec_1_hidden", "1"},
24647
+    {UNIMOD_Kdo, "spec_1_hidden", "1"},
24648
+    {UNIMOD_Kdo, "spec_1_position", "Anywhere"},
24649
+    {UNIMOD_Kdo, "spec_1_position", "Anywhere"},
24650
+    {UNIMOD_Kdo, "spec_1_site", "T"},
24651
+    {UNIMOD_Kdo, "spec_1_site", "S"},
24652
+    {UNIMOD_Andro_H2O, "approved", "0"},
24653
+    {UNIMOD_Andro_H2O, "delta_composition", "H(28) C(20) O(4)"},
24654
+    {UNIMOD_Andro_H2O, "spec_1_classification", "Chemical derivative"},
24655
+    {UNIMOD_Andro_H2O, "spec_1_hidden", "1"},
24656
+    {UNIMOD_Andro_H2O, "spec_1_position", "Anywhere"},
24657
+    {UNIMOD_Andro_H2O, "spec_1_site", "C"},
24658
+    {UNIMOD_His_O_2_, "approved", "0"},
24659
+    {UNIMOD_His_O_2_, "delta_composition", "H(7) C(6) N(3) O(3)"},
24660
+    {UNIMOD_His_O_2_, "spec_1_classification", "Post-translational"},
24661
+    {UNIMOD_His_O_2_, "spec_1_hidden", "1"},
24662
+    {UNIMOD_His_O_2_, "spec_1_position", "Anywhere"},
24663
+    {UNIMOD_His_O_2_, "spec_1_site", "H"},
24447 24664
 }; // propertyValue_
24448 24665
 
24449 24666
 
... ...
@@ -24495,13 +24712,13 @@ class CVTermData : public boost::singleton<CVTermData>
24495 24712
         cvMap_["PEFF"].URI = cvMap_["MS"].URI;
24496 24713
 
24497 24714
         cvMap_["MS"].id = "MS";
24498
-        cvMap_["MS"].version = "4.1.30";
24715
+        cvMap_["MS"].version = "4.1.41";
24499 24716
 
24500 24717
         cvMap_["PEFF"].id = "PEFF";
24501
-        cvMap_["PEFF"].version = "4.1.30";
24718
+        cvMap_["PEFF"].version = "4.1.41";
24502 24719
 
24503 24720
         cvMap_["UNIMOD"].id = "UNIMOD";
24504
-        cvMap_["UNIMOD"].version = "2019-09-10";
24721
+        cvMap_["UNIMOD"].version = "2020-06-09";
24505 24722
 
24506 24723
         cvMap_["UO"].id = "UO";
24507 24724
         cvMap_["UO"].version = "09:04:2014";
... ...
@@ -41,9 +41,9 @@
41 41
 // [psi-ms.obo]
42 42
 #define _PSI_MS_OBO_
43 43
 //   format-version: 1.2
44
-//   data-version: 4.1.30
45
-//   date: 30:08:2019 16:10
46
-//   saved-by: Gerhard Mayer
44
+//   data-version: 4.1.41
45
+//   date: 30:07:2020 18:25
46
+//   saved-by: Matt Chambers
47 47
 //   auto-generated-by: OBO-Edit 2.3.1
48 48
 //   import: http://ontologies.berkeleybop.org/pato.obo
49 49
 //   import: http://ontologies.berkeleybop.org/uo.obo
... ...
@@ -71,7 +71,7 @@
71 71
 // [unimod.obo]
72 72
 #define _UNIMOD_OBO_
73 73
 //   format-version: 1.2
74
-//   date: 2019:09:10 09:30
74
+//   date: 2020:06:09 11:01
75 75
 //
76 76
 // [unit.obo]
77 77
 #define _UNIT_OBO_
... ...
@@ -413,10 +413,10 @@ enum PWIZ_API_DECL CVID
413 413
     /// thomson (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
414 414
     MS_thomson = MS_m_z,
415 415
 
416
-    /// charge state: The charge state of the ion, single or multiple and positive or negatively charged.
416
+    /// charge state: Number of net charges, positive or negative, on an ion.
417 417
     MS_charge_state = 1000041,
418 418
 
419
-    /// z (charge state): The charge state of the ion, single or multiple and positive or negatively charged.
419
+    /// z (charge state): Number of net charges, positive or negative, on an ion.
420 420
     MS_z = MS_charge_state,
421 421
 
422 422
     /// peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
... ...
@@ -1082,8 +1082,8 @@ enum PWIZ_API_DECL CVID
1082 1082
     /// mass number: The sum of the protons and neutrons in an atom, molecule or ion.
1083 1083
     MS_mass_number_OBSOLETE = 1000223,
1084 1084
 
1085
-    /// molecular mass: The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules).
1086
-    MS_molecular_mass_OBSOLETE = 1000224,
1085
+    /// molecular mass: Mass of a molecule measured in unified atomic mass units (u or Da).
1086
+    MS_molecular_mass = 1000224,
1087 1087
 
1088 1088
     /// monoisotopic mass: The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.
1089 1089
     MS_monoisotopic_mass_OBSOLETE = 1000225,
... ...
@@ -1925,7 +1925,7 @@ enum PWIZ_API_DECL CVID
1925 1925
     /// scan: Function or process of the mass spectrometer where it records a spectrum.
1926 1926
     MS_scan = 1000441,
1927 1927
 
1928
-    /// spectrum: A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis.
1928
+    /// spectrum: Representation of intensity values corresponding to a range of measurement space.
1929 1929
     MS_spectrum = 1000442,
1930 1930
 
1931 1931
     /// mass analyzer type: Mass analyzer separates the ions according to their mass-to-charge ratio.
... ...
@@ -2111,16 +2111,16 @@ enum PWIZ_API_DECL CVID
2111 2111
     /// instrument attribute: Instrument properties that are associated with a value.
2112 2112
     MS_instrument_attribute = 1000496,
2113 2113
 
2114
-    /// zoom scan: Special scan mode, where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
2114
+    /// zoom scan: Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
2115 2115
     MS_zoom_scan = 1000497,
2116 2116
 
2117
-    /// enhanced resolution scan (zoom scan): Special scan mode, where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
2117
+    /// enhanced resolution scan (zoom scan): Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
2118 2118
     MS_enhanced_resolution_scan = MS_zoom_scan,
2119 2119
 
2120 2120
     /// full scan: Feature of the ion trap mass spectrometer where MS data is acquired over a mass range.
2121 2121
     MS_full_scan_OBSOLETE = 1000498,
2122 2122
 
2123
-    /// spectrum attribute: Spectrum properties that are associated with a value.
2123
+    /// spectrum attribute: Nonphysical characteristic attributed to a spectrum.
2124 2124
     MS_spectrum_attribute = 1000499,
2125 2125
 
2126 2126
     /// scan window upper limit: The lower m/z bound of a mass spectrometer scan window.
... ...
@@ -2132,7 +2132,7 @@ enum PWIZ_API_DECL CVID
2132 2132
     /// dwell time: The time spent gathering data across a peak.
2133 2133
     MS_dwell_time = 1000502,
2134 2134
 
2135
-    /// scan attribute: Scan properties that are associated with a value.
2135
+    /// scan attribute: Nonphysical characteristic attributed to a spectrum acquisition scan.
2136 2136
     MS_scan_attribute = 1000503,
2137 2137
 
2138 2138
     /// base peak m/z: M/z value of the signal of highest intensity in the mass spectrum.
... ...
@@ -2144,8 +2144,8 @@ enum PWIZ_API_DECL CVID
2144 2144
     /// ion role: Ion Role.
2145 2145
     MS_ion_role_OBSOLETE = 1000506,
2146 2146
 
2147
-    /// ion attribute: Ion properties that are associated with a value.
2148
-    MS_ion_attribute_OBSOLETE = 1000507,
2147
+    /// ion property: Nonphysical characteristic attributed to an ion.
2148
+    MS_ion_property = 1000507,
2149 2149
 
2150 2150
     /// ion chemical type: Ion Type.
2151 2151
     MS_ion_chemical_type_OBSOLETE = 1000508,
... ...
@@ -2156,7 +2156,7 @@ enum PWIZ_API_DECL CVID
2156 2156
     /// precursor activation attribute: Precursor Activation Attribute.
2157 2157
     MS_precursor_activation_attribute = 1000510,
2158 2158
 
2159
-    /// ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
2159
+    /// ms level: Stage number achieved in a multi stage mass spectrometry acquisition.
2160 2160
     MS_ms_level = 1000511,
2161 2161
 
2162 2162
     /// filter string: A string unique to Thermo instrument describing instrument settings for the scan.
... ...
@@ -2357,11 +2357,11 @@ enum PWIZ_API_DECL CVID
2357 2357
     /// no compression: No Compression.
2358 2358
     MS_no_compression = 1000576,
2359 2359
 
2360
-    /// raw data file: Describes the type of file and its content.
2361
-    MS_raw_data_file = 1000577,
2360
+    /// source data file: Data file from which an entity is sourced.
2361
+    MS_source_data_file = 1000577,
2362 2362
 
2363
-    /// source file (raw data file): Describes the type of file and its content.
2364
-    MS_source_file = MS_raw_data_file,
2363
+    /// source file (source data file): Data file from which an entity is sourced.
2364
+    MS_source_file = MS_source_data_file,
2365 2365
 
2366 2366
     /// LCQ Fleet: LCQ Fleet.
2367 2367
     MS_LCQ_Fleet = 1000578,
... ...
@@ -3092,7 +3092,7 @@ enum PWIZ_API_DECL CVID
3092 3092
     /// no combination: Use this term if only one scan was recorded or there is no information about scans available.
3093 3093
     MS_no_combination = 1000795,
3094 3094
 
3095
-    /// spectrum title: A free-form text title describing a spectrum.
3095
+    /// spectrum title: Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file.
3096 3096
     MS_spectrum_title = 1000796,
3097 3097
 
3098 3098
     /// peak list scans: A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
... ...
@@ -3290,14 +3290,14 @@ enum PWIZ_API_DECL CVID
3290 3290
     /// fraction identifier: Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information.
3291 3291
     MS_fraction_identifier = 1000858,
3292 3292
 
3293
-    /// molecule: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
3293
+    /// molecule: Group of two or more atoms held together by chemical bonds.
3294 3294
     MS_molecule = 1000859,
3295 3295
 
3296
-    /// peptide: A compound of low molecular weight that is composed of two or more amino acids.
3296
+    /// peptide: A molecule of low molecular weight that is composed of two or more amino acid residues.
3297 3297
     MS_peptide = 1000860,
3298 3298
 
3299
-    /// chemical compound attribute: A describable property of a chemical compound.
3300
-    MS_chemical_compound_attribute = 1000861,
3299
+    /// molecular entity property: A physical characteristic of a molecular entity.
3300
+    MS_molecular_entity_property = 1000861,
3301 3301
 
3302 3302
     /// isoelectric point: The pH of a solution at which a charged molecule does not migrate in an electric field.
3303 3303
     MS_isoelectric_point = 1000862,
... ...
@@ -3311,8 +3311,8 @@ enum PWIZ_API_DECL CVID
3311 3311
     /// predicted pI (predicted isoelectric point): The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
3312 3312
     MS_predicted_pI = MS_predicted_isoelectric_point,
3313 3313
 
3314
-    /// chemical compound formula: A combination of symbols used to express the chemical composition of a compound.
3315
-    MS_chemical_compound_formula = 1000864,
3314
+    /// chemical formula: A combination of symbols used to express the chemical composition of a molecule.
3315
+    MS_chemical_formula = 1000864,
3316 3316
 
3317 3317
     /// empirical formula: A chemical formula which expresses the proportions of the elements present in a substance.
3318 3318
     MS_empirical_formula = 1000865,
... ...
@@ -3323,8 +3323,8 @@ enum PWIZ_API_DECL CVID
3323 3323
     /// structural formula: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
3324 3324
     MS_structural_formula = 1000867,
3325 3325
 
3326
-    /// SMILES string: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
3327
-    MS_SMILES_string = 1000868,
3326
+    /// SMILES formula: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
3327
+    MS_SMILES_formula = 1000868,
3328 3328
 
3329 3329
     /// collision gas pressure: The gas pressure of the collision gas used for collisional excitation.
3330 3330
     MS_collision_gas_pressure = 1000869,
... ...
@@ -3362,47 +3362,47 @@ enum PWIZ_API_DECL CVID
3362 3362
     /// interchannel delay: The duration of intervals between scanning, during which the instrument configuration is switched.
3363 3363
     MS_interchannel_delay = 1000880,
3364 3364
 
3365
-    /// chemical compound: A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
3366
-    MS_chemical_compound = 1000881,
3365
+    /// molecular entity: Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
3366
+    MS_molecular_entity = 1000881,
3367 3367
 
3368
-    /// protein: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
3368
+    /// protein: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene.
3369 3369
     MS_protein = 1000882,
3370 3370
 
3371 3371
     /// protein short name: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
3372 3372
     MS_protein_short_name = 1000883,
3373 3373
 
3374
-    /// protein attribute: An nonphysical attribute describing a specific protein.
3374
+    /// protein attribute: An nonphysical characterstic attributed to a specific protein.
3375 3375
     MS_protein_attribute = 1000884,
3376 3376
 
3377
-    /// protein accession: Accession number for a specific protein in a database.
3377
+    /// protein accession: Identifier for a specific protein in a database.
3378 3378
     MS_protein_accession = 1000885,
3379 3379
 
3380 3380
     /// protein name: A long name describing the function of the protein.
3381 3381
     MS_protein_name = 1000886,
3382 3382
 
3383
-    /// peptide attribute: A nonphysical attribute that can be used to describe a peptide.
3383
+    /// peptide attribute: Nonphysical characteristic attributed to a peptide.
3384 3384
     MS_peptide_attribute = 1000887,
3385 3385
 
3386
-    /// unmodified peptide sequence: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
3387
-    MS_unmodified_peptide_sequence = 1000888,
3386
+    /// stripped peptide sequence: Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away.
3387
+    MS_stripped_peptide_sequence = 1000888,
3388 3388
 
3389
-    /// modified peptide sequence: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid modifications that are present.
3390
-    MS_modified_peptide_sequence = 1000889,
3389
+    /// peptidoform sequence: Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present.
3390
+    MS_peptidoform_sequence = 1000889,
3391 3391
 
3392
-    /// peptide labeling state: A state description of how a peptide might be isotopically or isobarically labelled.
3393
-    MS_peptide_labeling_state = 1000890,
3392
+    /// peptidoform labeling state: A state description of how a peptide might be isotopically or isobarically labelled.
3393
+    MS_peptidoform_labeling_state = 1000890,
3394 3394
 
3395
-    /// heavy labeled peptide: A peptide that has been created or labelled with some heavier-than-usual isotopes.
3396
-    MS_heavy_labeled_peptide = 1000891,
3395
+    /// heavy labeled peptidoform: A peptide that has been created or labelled with some heavier-than-usual isotopes.
3396
+    MS_heavy_labeled_peptidoform = 1000891,
3397 3397
 
3398
-    /// unlabeled peptide: A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".
3399
-    MS_unlabeled_peptide = 1000892,
3398
+    /// unlabeled peptidoform: A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".
3399
+    MS_unlabeled_peptidoform = 1000892,
3400 3400
 
3401
-    /// light labeled peptide (unlabeled peptide): A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".
3402
-    MS_light_labeled_peptide = MS_unlabeled_peptide,
3401
+    /// light labeled peptide (unlabeled peptidoform): A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\".
3402
+    MS_light_labeled_peptide = MS_unlabeled_peptidoform,
3403 3403
 
3404
-    /// peptide group label: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
3405
-    MS_peptide_group_label = 1000893,
3404
+    /// peptidoform group label: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
3405
+    MS_peptidoform_group_label = 1000893,
3406 3406
 
3407 3407
     /// retention time: A time interval from the start of chromatography when an analyte exits a chromatographic column.
3408 3408
     MS_retention_time = 1000894,
... ...
@@ -3812,10 +3812,10 @@ enum PWIZ_API_DECL CVID
3812 3812
     /// SEQUEST:Full: 
3813 3813
     MS_SEQUEST_Full = 1001111,
3814 3814
 
3815
-    /// n-terminal flanking residue: The residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.
3815
+    /// n-terminal flanking residue: Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.
3816 3816
     MS_n_terminal_flanking_residue = 1001112,
3817 3817
 
3818
-    /// c-terminal flanking residue: The residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.
3818
+    /// c-terminal flanking residue: Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.
3819 3819
     MS_c_terminal_flanking_residue = 1001113,
3820 3820
 
3821 3821
     /// retention time(s): Retention time of the spectrum from the source file.
... ...
@@ -6161,7 +6161,7 @@ enum PWIZ_API_DECL CVID
6161 6161
     /// Velos Plus: Thermo Scientific second generation Velos.
6162 6162
     MS_Velos_Plus = 1001909,
6163 6163
 
6164
-    /// LTQ Orbitrap Elite: Thermo Scientific second generation Velos and Orbitrap.
6164
+    /// LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite.
6165 6165
     MS_LTQ_Orbitrap_Elite = 1001910,
6166 6166
 
6167 6167
     /// Q Exactive: Thermo Scientific Q Exactive.
... ...
@@ -8858,7 +8858,7 @@ enum PWIZ_API_DECL CVID
8858 8858
     /// 8800 Triple Quadrupole ICP-MS: The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer.
8859 8859
     MS_8800_Triple_Quadrupole_ICP_MS = 1002805,
8860 8860
 
8861
-    /// ion: An atomic or molecular species having a net positive or negative electric charge.
8861
+    /// ion: Molecular entity having a net positive or negative electric charge.
8862 8862
     MS_ion = 1002806,
8863 8863
 
8864 8864
     /// positive mode adduct ion: Adduct ion with positive ionization.
... ...
@@ -8867,11 +8867,11 @@ enum PWIZ_API_DECL CVID
8867 8867
     /// negative mode adduct ion: Adduct ion with negative ionization.
8868 8868
     MS_negative_mode_adduct_ion = 1002808,
8869 8869
 
8870
-    /// adduct ion attribute: Attribute describing an adduct formation.
8870
+    /// adduct ion attribute: Nonphysical characteristic attributed to an adduct ion.
8871 8871
     MS_adduct_ion_attribute = 1002809,
8872 8872
 
8873
-    /// adduct ion mass: Mass of an adduct formation specified by the given value.
8874
-    MS_adduct_ion_mass = 1002810,
8873
+    /// adduct ion X m/z: Theoretical m/z of the X component in the adduct M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator.
8874
+    MS_adduct_ion_X_m_z = 1002810,
8875 8875
 
8876 8876
     /// adduct ion isotope: Isotope of the matrix molecule M of an adduct formation.
8877 8877
     MS_adduct_ion_isotope = 1002811,
... ...
@@ -8879,7 +8879,7 @@ enum PWIZ_API_DECL CVID
8879 8879
     /// Regular expression for adduct ion formula: (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]).
8880 8880
     MS_Regular_expression_for_adduct_ion_formula = 1002812,
8881 8881
 
8882
-    /// adduct ion formula: Adduct formation formula specified by the given value.
8882
+    /// adduct ion formula: Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression.
8883 8883
     MS_adduct_ion_formula = 1002813,
8884 8884
 
8885 8885
     /// volt-second per square centimeter: An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm].
... ...
@@ -8903,10 +8903,10 @@ enum PWIZ_API_DECL CVID
8903 8903
     /// Bruker TDF nativeID format, combined spectra: Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation.
8904 8904
     MS_Bruker_TDF_nativeID_format__combined_spectra = 1002819,
8905 8905
 
8906
-    /// M+H ion: M+H ion from positive ion mode (M in the property ionMass denotes the mass of the neutral molecule).
8906
+    /// M+H ion: Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton.
8907 8907
     MS_M_H_ion_1002820 = 1002820,
8908 8908
 
8909
-    /// M-H ion: M-H ion from negative ion mode (M in the property ionMass denotes the mass of the neutral molecule).
8909
+    /// M-H ion: Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M.
8910 8910
     MS_M_H_ion_1002821 = 1002821,
8911 8911
 
8912 8912
     /// OpenMS file format: File format developed by the OpenMS team.
... ...
@@ -9011,10 +9011,10 @@ enum PWIZ_API_DECL CVID
9011 9011
     /// Non peer-reviewed dataset: Dataset that has not been peer-reviewed by any means.
9012 9012
     MS_Non_peer_reviewed_dataset = 1002855,
9013 9013
 
9014
-    /// Supported dataset by repository: The PX dataset is supported by and is available through the submission repository.
9014
+    /// Supported dataset by repository: Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission.
9015 9015
     MS_Supported_dataset_by_repository = 1002856,
9016 9016
 
9017
-    /// Unsupported dataset by repository: The PX dataset is not fully supported by the submission repository.
9017
+    /// Unsupported dataset by repository: Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission.
9018 9018
     MS_Unsupported_dataset_by_repository = 1002857,
9019 9019
 
9020 9020
     /// Dataset with its publication pending: A dataset which has an associated manuscript pending for publication.
... ...
@@ -9479,7 +9479,7 @@ enum PWIZ_API_DECL CVID
9479 9479
     /// MSFragger: A database search-based peptide identification tool.
9480 9480
     MS_MSFragger = 1003014,
9481 9481
 
9482
-    /// razor peptide: A peptide which is shared between protein groups and assigned to the protein group with the largest number of identified peptides.
9482
+    /// razor peptide: Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides.
9483 9483
     MS_razor_peptide = 1003015,
9484 9484
 
9485 9485
     /// ProteinProphet:peptide weight: Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins.
... ...
@@ -9527,6 +9527,252 @@ enum PWIZ_API_DECL CVID
9527 9527
     /// Mascot:MinNumSigUniqueSeqs: Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'.
9528 9528
     MS_Mascot_MinNumSigUniqueSeqs = 1003030,
9529 9529
 
9530
+    /// CPTAC accession number: Main identifier of a CPTAC dataset.
9531
+    MS_CPTAC_accession_number = 1003031,
9532
+
9533
+    /// compound identification confidence code in MS-DIAL: The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program.
9534
+    MS_compound_identification_confidence_code_in_MS_DIAL = 1003032,
9535
+
9536
+    /// molecular entity attribute: Non-inherent characteristic attributed to a molecular entity.
9537
+    MS_molecular_entity_attribute = 1003033,
9538
+
9539
+    /// atom: Smallest constituent unit of ordinary matter that constitutes a chemical element.
9540
+    MS_atom = 1003034,
9541
+
9542
+    /// small molecule: Low molecular weight (< 900 daltons) organic compound that may regulate a biological process.
9543
+    MS_small_molecule = 1003035,
9544
+
9545
+    /// metabolite: Small molecule that is the intermediate end product of metabolism.
9546
+    MS_metabolite = 1003036,
9547
+
9548
+    /// ribonucleotide: Nucleotide containing ribose as its pentose component.
9549
+    MS_ribonucleotide = 1003037,
9550
+
9551
+    /// deoxyribonucleotide: Monomer, or single unit, of DNA, or deoxyribonucleic acid.
9552
+    MS_deoxyribonucleotide = 1003038,
9553
+
9554
+    /// amino acid: Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid.
9555
+    MS_amino_acid = 1003039,
9556
+
9557
+    /// monosaccharide: Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule.
9558
+    MS_monosaccharide = 1003040,
9559
+
9560
+    /// nucleic acid: Molecule composed of a chain of nucleotides.
9561
+    MS_nucleic_acid = 1003041,
9562
+
9563
+    /// polysaccharide: Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages.
9564
+    MS_polysaccharide = 1003042,
9565
+
9566
+    /// number of residues: Number of amino acid residues in a peptide, commonly referred to as the peptide length.
9567
+    MS_number_of_residues = 1003043,
9568
+
9569
+    /// number of missed cleavages: Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not.
9570
+    MS_number_of_missed_cleavages = 1003044,
9571
+
9572
+    /// peptide-to-protein mapping: Process of mapping a peptide sequence to a protein sequence.
9573
+    MS_peptide_to_protein_mapping = 1003045,
9574
+
9575
+    /// peptide-to-protein mapping attribute: Nonphysical characteristic attributed to the result of peptide-to-protein mapping.
9576
+    MS_peptide_to_protein_mapping_attribute = 1003046,
9577
+
9578
+    /// protein sequence offset: Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence.
9579
+    MS_protein_sequence_offset = 1003047,
9580
+
9581
+    /// number of enzymatic termini: Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules.
9582
+    MS_number_of_enzymatic_termini = 1003048,
9583
+
9584
+    /// peptidoform: Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations.
9585
+    MS_peptidoform = 1003049,
9586
+
9587
+    /// peptidoform attribute: Non-inherent characteristic attributed to a peptidoform.
9588
+    MS_peptidoform_attribute = 1003050,
9589
+
9590
+    /// peptidoform ion: Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'.
9591
+    MS_peptidoform_ion = 1003051,
9592
+
9593
+    /// peptidoform ion property: Inherent or measurable characteristic of a peptidoform ion.
9594
+    MS_peptidoform_ion_property = 1003052,
9595
+
9596
+    /// theoretical monoisotopic m/z: Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents.
9597
+    MS_theoretical_monoisotopic_m_z = 1003053,
9598
+
9599
+    /// theoretical average m/z: Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes.
9600
+    MS_theoretical_average_m_z = 1003054,
9601
+
9602
+    /// adduct: Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species.
9603
+    MS_adduct = 1003055,
9604
+
9605
+    /// adduct ion property: Physical measurable characteristic of an adduct ion.
9606
+    MS_adduct_ion_property = 1003056,
9607
+
9608
+    /// scan number: Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run.
9609
+    MS_scan_number = 1003057,
9610
+
9611
+    /// spectrum property: Inherent or measurable characteristic of a spectrum.
9612
+    MS_spectrum_property = 1003058,
9613
+
9614
+    /// number of peaks: Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points.
9615
+    MS_number_of_peaks = 1003059,
9616
+
9617
+    /// number of data points: Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks.
9618
+    MS_number_of_data_points = 1003060,
9619
+
9620
+    /// spectrum name: Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection.
9621
+    MS_spectrum_name = 1003061,
9622
+
9623
+    /// spectrum index: Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0.
9624
+    MS_spectrum_index = 1003062,
9625
+
9626
+    /// universal spectrum identifier: PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library.
9627
+    MS_universal_spectrum_identifier = 1003063,
9628
+
9629
+    /// spectrum aggregation attribute: Non-inherent characteristic attributed to spectrum aggregation.
9630
+    MS_spectrum_aggregation_attribute = 1003064,
9631
+
9632
+    /// spectrum aggregation type: Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.).
9633
+    MS_spectrum_aggregation_type = 1003065,
9634
+
9635
+    /// singleton spectrum: Spectrum that is not the result of some aggregation process.
9636
+    MS_singleton_spectrum = 1003066,
9637
+
9638
+    /// consensus spectrum: Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates.
9639
+    MS_consensus_spectrum = 1003067,
9640
+
9641
+    /// best replicate spectrum: Spectrum that is considered the most representative from a pool of replicate spectra.
9642
+    MS_best_replicate_spectrum = 1003068,
9643
+
9644
+    /// number of replicate spectra available: Number of replicate spectra available for use during the aggregation process.
9645
+    MS_number_of_replicate_spectra_available = 1003069,
9646
+
9647
+    /// number of replicate spectra used: Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm.
9648
+    MS_number_of_replicate_spectra_used = 1003070,
9649
+
9650
+    /// spectrum origin attribute: Non-inherent characteristic attributed to spectrum aggregation.
9651
+    MS_spectrum_origin_attribute = 1003071,
9652
+
9653
+    /// spectrum origin type: Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.).
9654
+    MS_spectrum_origin_type = 1003072,
9655
+
9656
+    /// observed spectrum: Spectrum that originates from an analysis attempt of a single analyte species on an instrument.
9657
+    MS_observed_spectrum = 1003073,
9658
+
9659
+    /// predicted spectrum: Spectrum that originates from a compututational algorithm that attempts to predict spectra.
9660
+    MS_predicted_spectrum = 1003074,
9661
+
9662
+    /// demultiplexed spectrum: Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species.
9663
+    MS_demultiplexed_spectrum = 1003075,
9664
+
9665
+    /// uninterpreted spectrum: Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features.
9666
+    MS_uninterpreted_spectrum = 1003076,
9667
+
9668
+    /// interpreted spectrum: Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature.
9669
+    MS_interpreted_spectrum = 1003077,
9670
+
9671
+    /// interpreted spectrum attribute: Non-inherent characteristic attributed to an interpreted spectrum.
9672
+    MS_interpreted_spectrum_attribute = 1003078,
9673
+
9674
+    /// total unassigned intensity fraction: Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum.
9675
+    MS_total_unassigned_intensity_fraction = 1003079,
9676
+
9677
+    /// top 20 peak unassigned intensity fraction: Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum.
9678
+    MS_top_20_peak_unassigned_intensity_fraction = 1003080,
9679
+
9680
+    /// unidentified modification monoisotopic mass delta: Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML.
9681
+    MS_unidentified_modification_monoisotopic_mass_delta = 1003081,
9682
+
9683
+    /// MS-DIAL: Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors.
9684
+    MS_MS_DIAL = 1003082,
9685
+
9686
+    /// raw data file: Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file).
9687
+    MS_raw_data_file = 1003083,
9688
+
9689
+    /// processed data file: File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument.
9690
+    MS_processed_data_file = 1003084,
9691
+
9692
+    /// previous MSn-1 scan precursor intensity: Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes.
9693
+    MS_previous_MSn_1_scan_precursor_intensity = 1003085,
9694
+
9695
+    /// precursor apex intensity: Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope.
9696
+    MS_precursor_apex_intensity = 1003086,
9697
+
9698
+    /// supported by repository but incomplete data and/or metadata: Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available.
9699
+    MS_supported_by_repository_but_incomplete_data_and_or_metadata = 1003087,
9700
+
9701
+    /// truncation and zlib compression: Data array compression using mantissa bit truncation followed by zlib compression.
9702
+    MS_truncation_and_zlib_compression = 1003088,
9703
+
9704
+    /// truncation, delta prediction and zlib compression: Data array compression using mantissa bit truncation, delta prediction and zlib compression.
9705
+    MS_truncation__delta_prediction_and_zlib_compression = 1003089,
9706
+
9707
+    /// truncation, linear prediction and zlib compression: Data array compression using mantissa bit truncation, linear prediction and zlib compression.
9708
+    MS_truncation__linear_prediction_and_zlib_compression = 1003090,
9709
+
9710
+    /// binary data compression parameter: Settable parameter for a binary data compression event.
9711
+    MS_binary_data_compression_parameter = 1003091,
9712
+
9713
+    /// number of mantissa bits truncated: Number of extraneous mantissa bits truncated to improve subsequent compression.
9714
+    MS_number_of_mantissa_bits_truncated = 1003092,
9715
+
9716
+    /// Lys-N: Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues.
9717
+    MS_Lys_N = 1003093,
9718
+
9719
+    /// Orbitrap Exploris 240: Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS.
9720
+    MS_Orbitrap_Exploris_240 = 1003094,
9721
+
9722
+    /// Orbitrap Exploris 120: Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS.
9723
+    MS_Orbitrap_Exploris_120 = 1003095,
9724
+
9725
+    /// LTQ Orbitrap Velos Pro: Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro.
9726
+    MS_LTQ_Orbitrap_Velos_Pro = 1003096,
9727
+
9728
+    /// MaxQuant protein group-level score: The probability based MaxQuant protein group score.
9729
+    MS_MaxQuant_protein_group_level_score = 1003097,
9730
+
9731
+    /// Andromeda peptide PEP: Peptide probability from Andromeda.
9732
+    MS_Andromeda_peptide_PEP = 1003098,
9733
+
9734
+    /// MaxQuant-DIA peptide PEP: Peptide probability from MaxQuant-DIA algorithm.
9735
+    MS_MaxQuant_DIA_peptide_PEP = 1003099,
9736
+
9737
+    /// MaxQuant-DIA score: PSM evidence score from MaxQuant-DIA algorithm.
9738
+    MS_MaxQuant_DIA_score = 1003100,
9739
+
9740
+    /// MaxQuant-DIA PEP: PSM evidence PEP probability from MaxQuant-DIA algorithm.
9741
+    MS_MaxQuant_DIA_PEP = 1003101,
9742
+
9743
+    /// NIST msp comment: Term for a comment field withing the NIST msp file format
9744
+    MS_NIST_msp_comment = 1003102,
9745
+
9746
+    /// ion interpretation format: Interpretation format used for annotating individual spectrum ion peaks.
9747
+    MS_ion_interpretation_format = 1003103,
9748
+
9749
+    /// peptide ion interpretation format: Interpretation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions.
9750
+    MS_peptide_ion_interpretation_format = 1003104,
9751
+
9752
+    /// cross-linked peptide ion interpretation format: Interpretation format designed specifically for cross-linked peptide ion peaks.
9753
+    MS_cross_linked_peptide_ion_interpretation_format = 1003105,
9754
+
9755
+    /// glycan ion interpretation format: Interpretation format designed specifically for glycan ion peaks.
9756
+    MS_glycan_ion_interpretation_format = 1003106,
9757
+
9758
+    /// lipid ion interpretation format: Interpretation format designed specifically for lipid ion peaks.
9759
+    MS_lipid_ion_interpretation_format = 1003107,
9760
+
9761
+    /// PatternLab: PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data.
9762
+    MS_PatternLab = 1003108,
9763
+
9764
+    /// SIM-XL: Identifying cross-linked peptides in complex protein mixtures
9765
+    MS_SIM_XL = 1003109,
9766
+
9767
+    /// SIM-XL score: SIM-XL identification search engine score
9768
+    MS_SIM_XL_score = 1003110,
9769
+
9770
+    /// QUIN-XL: Quantification of cross-linked peptides in complex protein mixtures
9771
+    MS_QUIN_XL = 1003111,
9772
+
9773
+    /// Orbitrap ID-X: Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
9774
+    MS_Orbitrap_ID_X = 1003112,
9775
+
9530 9776
     /// unimod root node: The root node of the unimod modifications ontology.
9531 9777
     UNIMOD_unimod_root_node = 200000000,
9532 9778
 
... ...
@@ -12263,7 +12509,7 @@ enum PWIZ_API_DECL CVID
12263 12509
     /// Label:13C(3): 13C3 label for SILAC.
12264 12510
     UNIMOD_Label_13C_3_ = 200001296,
12265 12511
 
12266
-    /// Label:13C(3)15N(1): 13C3 15N1 label for SILAC.
12512
+    /// Label:13C(3)15N(1): SILAC or AQUA label.
12267 12513
     UNIMOD_Label_13C_3_15N_1_ = 200001297,
12268 12514
 
12269 12515
     /// Label:13C(4)15N(1): 13C4 15N1 label for SILAC.
... ...
@@ -12428,7 +12674,7 @@ enum PWIZ_API_DECL CVID
12428 12674
     /// Homocysteic_acid: Methionine oxidation to homocysteic acid.
12429 12675
     UNIMOD_Homocysteic_acid = 200001384,
12430 12676
 
12431
-    /// Hydroxamic_acid: Conversion of carboxylic acid to hydroxamic acid.
12677
+    /// Hydroxamic_acid: ADP-ribosylation followed by conversion to hydroxamic acid via hydroxylamine.
12432 12678
     UNIMOD_Hydroxamic_acid = 200001385,
12433 12679
 
12434 12680
     /// 3-phosphoglyceryl: 3-phosphoglyceryl.
... ...
@@ -13988,6 +14234,15 @@ enum PWIZ_API_DECL CVID
13988 14234
     /// TMTpro_zero: Native TMTpro Tandem Mass Tag.
13989 14235
     UNIMOD_TMTpro_zero = 200002017,
13990 14236
 
14237
+    /// Kdo: Glycosylation with KDO.
14238
+    UNIMOD_Kdo = 200002022,
14239
+
14240
+    /// Andro-H2O: Andrographolide with the loss of H2O.
14241
+    UNIMOD_Andro_H2O = 200002025,
14242
+
14243
+    /// His+O(2): Photo-induced histidine adduct.
14244
+    UNIMOD_His_O_2_ = 200002027,
14245
+
13991 14246
     /// unit: A unit of measurement is a standardized quantity of a physical quality.
13992 14247
     UO_unit = 300000000,
13993 14248
 
... ...
@@ -14106,7 +14361,7 @@ enum PWIZ_API_DECL CVID
14106 14361
     UO_microampere = 300000038,
14107 14362
 
14108 14363
     /// micromole: A substance unit equal to a millionth of a mol or 10^[-6] mol.
14109
-    UO_micromole = 300000039,
14364
+    UO_micromole_300000039 = 300000039,
14110 14365
 
14111 14366
     /// millimole: A substance unit equal to a thousandth of a mol or 10^[-3] mol.
14112 14367
     UO_millimole = 300000040,
... ...
@@ -15120,7 +15375,13 @@ enum PWIZ_API_DECL CVID
15120 15375
     UO_united_states_customary_cup = 300010046,
15121 15376
 
15122 15377
     /// united states fda cup: A United States FDA cup is a unit of measurement of volume used by the US Federal Department of Agriculture as a nutritional serving measure. It equals a 240 mL volume.
15123
-    UO_united_states_fda_cup = 300010047
15378
+    UO_united_states_fda_cup = 300010047,
15379
+
15380
+    /// micromole: A substance unit which is equal to one millionth of a mole.
15381
+    UO_micromole_300010048 = 300010048,
15382
+
15383
+    /// gram per square meter: An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared.
15384
+    UO_gram_per_square_meter = 300010049
15124 15385
 }; // enum CVID
15125 15386
 
15126 15387
 
... ...
@@ -1,7 +1,7 @@
1 1
 format-version: 1.2
2
-data-version: 4.1.30
3
-date: 30:08:2019 16:10
4
-saved-by: Gerhard Mayer
2
+data-version: 4.1.41
3
+date: 30:07:2020 18:25
4
+saved-by: Matt Chambers
5 5
 auto-generated-by: OBO-Edit 2.3.1
6 6
 import: http://ontologies.berkeleybop.org/pato.obo
7 7
 import: http://ontologies.berkeleybop.org/uo.obo
... ...
@@ -342,10 +342,11 @@ is_a: UO:0000000 ! unit
342 342
 [Term]
343 343
 id: MS:1000041
344 344
 name: charge state
345
-def: "The charge state of the ion, single or multiple and positive or negatively charged." [PSI:MS]
345
+def: "Number of net charges, positive or negative, on an ion." [PSI:MS]
346 346
 synonym: "z" EXACT []
347 347
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
348 348
 is_a: MS:1000455 ! ion selection attribute
349
+is_a: MS:1000507 ! ion property
349 350
 
350 351
 [Term]
351 352
 id: MS:1000042
... ...
@@ -1553,11 +1554,10 @@ is_obsolete: true
1553 1554
 [Term]
1554 1555
 id: MS:1000224
1555 1556
 name: molecular mass
1556
-def: "OBSOLETE The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules)." [PSI:MS]
1557
+def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass]
1557 1558
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
1558
-comment: This child of the former purgatory term ion attribute was made obsolete.
1559
+is_a: MS:1000861 ! molecular entity property
1559 1560
 relationship: has_units UO:0000002 ! mass unit
1560
-is_obsolete: true
1561 1561
 
1562 1562
 [Term]
1563 1563
 id: MS:1000225
... ...
@@ -2014,7 +2014,7 @@ name: total ion current
2014 2014
 def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS]
2015 2015
 synonym: "TIC" EXACT []
2016 2016
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
2017
-is_a: MS:1000499 ! spectrum attribute
2017
+is_a: MS:1003058 ! spectrum property
2018 2018
 
2019 2019
 [Term]
2020 2020
 id: MS:1000286
... ...
@@ -2482,7 +2482,7 @@ is_obsolete: true
2482 2482
 id: MS:1000353
2483 2483
 name: adduct ion
2484 2484
 def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS]
2485
-is_a: MS:1002806 ! ion
2485
+is_a: MS:1003055 ! adduct
2486 2486
 
2487 2487
 [Term]
2488 2488
 id: MS:1000354
... ...
@@ -3074,7 +3074,7 @@ relationship: part_of MS:1001458 ! spectrum generation information
3074 3074
 [Term]
3075 3075
 id: MS:1000442
3076 3076
 name: spectrum
3077
-def: "A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis." [PSI:MS]
3077
+def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS]
3078 3078
 relationship: part_of MS:1001458 ! spectrum generation information
3079 3079
 
3080 3080
 [Term]
... ...
@@ -3426,9 +3426,9 @@ relationship: part_of MS:1000463 ! instrument
3426 3426
 [Term]
3427 3427
 id: MS:1000497
3428 3428
 name: zoom scan
3429
-def: "Special scan mode, where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS]
3429
+def: "Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS]
3430 3430
 synonym: "enhanced resolution scan" EXACT []
3431
-is_a: MS:1000499 ! spectrum attribute
3431
+is_a: MS:1000503 ! scan attribute
3432 3432
 
3433 3433
 [Term]
3434 3434
 id: MS:1000498
... ...
@@ -3440,8 +3440,7 @@ is_obsolete: true
3440 3440
 [Term]
3441 3441
 id: MS:1000499
3442 3442
 name: spectrum attribute
3443
-def: "Spectrum properties that are associated with a value." [PSI:MS]
3444
-is_a: MS:1000547 ! object attribute
3443
+def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS]
3445 3444
 relationship: part_of MS:1000442 ! spectrum
3446 3445
 
3447 3446
 [Term]
... ...
@@ -3475,7 +3474,7 @@ relationship: has_units UO:0000031 ! minute
3475 3474
 [Term]
3476 3475
 id: MS:1000503
3477 3476
 name: scan attribute
3478
-def: "Scan properties that are associated with a value." [PSI:MS]
3477
+def: "Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS]
3479 3478
 is_a: MS:1000547 ! object attribute
3480 3479
 relationship: part_of MS:1000441 ! scan
3481 3480
 
... ...
@@ -3484,7 +3483,7 @@ id: MS:1000504
3484 3483
 name: base peak m/z
3485 3484
 def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS]
3486 3485
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
3487
-is_a: MS:1000499 ! spectrum attribute
3486
+is_a: MS:1003058 ! spectrum property
3488 3487
 relationship: has_units MS:1000040 ! m/z
3489 3488
 
3490 3489
 [Term]
... ...
@@ -3492,7 +3491,7 @@ id: MS:1000505
3492 3491
 name: base peak intensity
3493 3492
 def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS]
3494 3493
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
3495
-is_a: MS:1000499 ! spectrum attribute
3494
+is_a: MS:1003058 ! spectrum property
3496 3495
 relationship: has_units MS:1000131 ! number of detector counts
3497 3496
 relationship: has_units MS:1000132 ! percent of base peak
3498 3497
 relationship: has_units MS:1000814 ! counts per second
... ...
@@ -3508,10 +3507,9 @@ is_obsolete: true
3508 3507
 
3509 3508
 [Term]
3510 3509
 id: MS:1000507
3511
-name: ion attribute
3512
-def: "OBSOLETE Ion properties that are associated with a value." [PSI:MS]
3513
-comment: This child of the former purgatory term ion was made obsolete.
3514
-is_obsolete: true
3510
+name: ion property
3511
+def: "Nonphysical characteristic attributed to an ion." [PSI:MS]
3512
+relationship: part_of MS:1002806 ! ion
3515 3513
 
3516 3514
 [Term]
3517 3515
 id: MS:1000508
... ...
@@ -3537,7 +3535,7 @@ relationship: part_of MS:1000456 ! precursor activation
3537 3535
 [Term]
3538 3536
 id: MS:1000511
3539 3537
 name: ms level
3540
-def: "Stages of ms achieved in a multi stage mass spectrometry experiment." [PSI:MS]
3538
+def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS]
3541 3539
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
3542 3540
 is_a: MS:1000499 ! spectrum attribute
3543 3541
 
... ...
@@ -3634,7 +3632,7 @@ is_a: MS:1000518 ! binary data type
3634 3632
 id: MS:1000524
3635 3633
 name: data file content
3636 3634
 def: "Describes the data content on the file." [PSI:MS]
3637
-relationship: part_of MS:1000577 ! raw data file
3635
+relationship: part_of MS:1000577 ! source data file
3638 3636
 
3639 3637
 [Term]
3640 3638
 id: MS:1000525
... ...
@@ -3653,8 +3651,8 @@ id: MS:1000527
3653 3651
 name: highest observed m/z
3654 3652
 def: "Highest m/z value observed in the m/z array." [PSI:MS]
3655 3653
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
3656
-is_a: MS:1000499 ! spectrum attribute
3657 3654
 is_a: MS:1000808 ! chromatogram attribute
3655
+is_a: MS:1003058 ! spectrum property
3658 3656
 relationship: has_units MS:1000040 ! m/z
3659 3657
 
3660 3658
 [Term]
... ...
@@ -3662,8 +3660,8 @@ id: MS:1000528
3662 3660
 name: lowest observed m/z
3663 3661
 def: "Lowest m/z value observed in the m/z array." [PSI:MS]
3664 3662
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
3665
-is_a: MS:1000499 ! spectrum attribute
3666 3663
 is_a: MS:1000808 ! chromatogram attribute
3664
+is_a: MS:1003058 ! spectrum property
3667 3665
 relationship: has_units MS:1000040 ! m/z
3668 3666
 
3669 3667
 [Term]
... ...
@@ -3892,7 +3890,7 @@ is_a: MS:1001459 ! file format
3892 3890
 id: MS:1000561
3893 3891
 name: data file checksum type
3894 3892
 def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS]
3895
-relationship: part_of MS:1000577 ! raw data file
3893
+relationship: part_of MS:1000577 ! source data file
3896 3894
 
3897 3895
 [Term]
3898 3896
 id: MS:1000562
... ...
@@ -3989,10 +3987,11 @@ is_a: MS:1000572 ! binary data compression type
3989 3987
 
3990 3988
 [Term]
3991 3989
 id: MS:1000577
3992
-name: raw data file
3993
-def: "Describes the type of file and its content." [PSI:MS]
3990
+name: source data file
3991
+def: "Data file from which an entity is sourced." [PSI:MS]
3994 3992
 synonym: "source file" EXACT []
3995 3993
 relationship: part_of MS:1001458 ! spectrum generation information
3994
+is_a: MS:1000499 ! spectrum attribute
3996 3995
 
3997 3996
 [Term]
3998 3997
 id: MS:1000578
... ...
@@ -4274,7 +4273,7 @@ id: MS:1000618
4274 4273
 name: highest observed wavelength
4275 4274
 def: "Highest wavelength observed in an EMR spectrum." [PSI:MS]
4276 4275
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
4277
-is_a: MS:1000499 ! spectrum attribute
4276
+is_a: MS:1003058 ! spectrum property
4278 4277
 is_a: MS:1000808 ! chromatogram attribute
4279 4278
 relationship: has_units UO:0000018 ! nanometer
4280 4279
 
... ...
@@ -4283,7 +4282,7 @@ id: MS:1000619
4283 4282
 name: lowest observed wavelength
4284 4283
 def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS]
4285 4284
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
4286
-is_a: MS:1000499 ! spectrum attribute
4285
+is_a: MS:1003058 ! spectrum property
4287 4286
 is_a: MS:1000808 ! chromatogram attribute
4288 4287
 relationship: has_units UO:0000018 ! nanometer
4289 4288
 
... ...
@@ -5284,7 +5283,7 @@ id: MS:1000767
5284 5283
 name: native spectrum identifier format
5285 5284
 def: "Describes how the native spectrum identifiers are formated." [PSI:MS]
5286 5285
 synonym: "nativeID format" EXACT []
5287
-relationship: part_of MS:1000577 ! raw data file
5286
+relationship: part_of MS:1000577 ! source data file
5288 5287
 
5289 5288
 [Term]
5290 5289
 id: MS:1000768
... ...
@@ -5495,11 +5494,11 @@ is_a: MS:1000570 ! spectra combination
5495 5494
 [Term]
5496 5495
 id: MS:1000796
5497 5496
 name: spectrum title
5498
-def: "A free-form text title describing a spectrum." [PSI:MS]
5497
+def: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS]
5499 5498
 comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list.
5500 5499
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
5501
-is_a: MS:1000499 ! spectrum attribute
5502 5500
 is_a: MS:1001405 ! spectrum identification result details
5501
+is_a: MS:1000499 ! spectrum attribute
5503 5502
 
5504 5503
 [Term]
5505 5504
 id: MS:1000797
... ...
@@ -5507,8 +5506,8 @@ name: peak list scans
5507 5506
 def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
5508 5507
 comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list.
5509 5508
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
5510
-is_a: MS:1000499 ! spectrum attribute
5511 5509
 is_a: MS:1001405 ! spectrum identification result details
5510
+is_a: MS:1003058 ! spectrum property
5512 5511
 
5513 5512
 [Term]
5514 5513
 id: MS:1000798
... ...
@@ -5516,8 +5515,8 @@ name: peak list raw scans
5516 5515
 def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
5517 5516
 comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list.
5518 5517
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
5519
-is_a: MS:1000499 ! spectrum attribute
5520 5518
 is_a: MS:1001405 ! spectrum identification result details
5519
+is_a: MS:1003058 ! spectrum property
5521 5520
 
5522 5521
 [Term]
5523 5522
 id: MS:1000799
... ...
@@ -5934,20 +5933,20 @@ is_a: MS:1000857 ! run attribute
5934 5933
 [Term]
5935 5934
 id: MS:1000859
5936 5935
 name: molecule
5937
-def: "A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction." [PSI:MS]
5938
-relationship: part_of MS:1000881 ! chemical compound
5936
+def: "Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule]
5937
+is_a: MS:1000881 ! molecular entity
5939 5938
 
5940 5939
 [Term]
5941 5940
 id: MS:1000860
5942 5941
 name: peptide
5943
-def: "A compound of low molecular weight that is composed of two or more amino acids." [PSI:MS]
5944
-is_a: MS:1000881 ! chemical compound
5942
+def: "A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS]
5943
+is_a: MS:1000859 ! molecule
5945 5944
 
5946 5945
 [Term]
5947 5946
 id: MS:1000861
5948
-name: chemical compound attribute
5949
-def: "A describable property of a chemical compound." [PSI:MS]
5950
-relationship: part_of MS:1000881 ! chemical compound
5947
+name: molecular entity property
5948
+def: "A physical characteristic of a molecular entity." [PSI:MS]
5949
+relationship: part_of MS:1000881 ! molecular entity
5951 5950
 
5952 5951
 [Term]
5953 5952
 id: MS:1000862
... ...
@@ -5955,7 +5954,7 @@ name: isoelectric point
5955 5954
 def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS]
5956 5955
 synonym: "pI" EXACT []
5957 5956
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
5958
-is_a: MS:1000861 ! chemical compound attribute
5957
+is_a: MS:1000861 ! molecular entity property
5959 5958
 
5960 5959
 [Term]
5961 5960
 id: MS:1000863
... ...
@@ -5967,37 +5966,37 @@ is_a: MS:1000862 ! isoelectric point
5967 5966
 
5968 5967
 [Term]
5969 5968
 id: MS:1000864
5970
-name: chemical compound formula
5971
-def: "A combination of symbols used to express the chemical composition of a compound." [PSI:MS]
5972
-relationship: part_of MS:1000881 ! chemical compound
5969
+name: chemical formula
5970
+def: "A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846]
5971
+is_a: MS:1003033 ! molecular entity attribute
5973 5972
 
5974 5973
 [Term]
5975 5974
 id: MS:1000865
5976 5975
 name: empirical formula
5977 5976
 def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS]
5978 5977
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
5979
-is_a: MS:1000864 ! chemical compound formula
5978
+is_a: MS:1000864 ! chemical formula
5980 5979
 
5981 5980
 [Term]
5982 5981
 id: MS:1000866
5983 5982
 name: molecular formula
5984 5983
 def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS]
5985 5984
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
5986
-is_a: MS:1000864 ! chemical compound formula
5985
+is_a: MS:1000864 ! chemical formula
5987 5986
 
5988 5987
 [Term]
5989 5988
 id: MS:1000867
5990 5989
 name: structural formula
5991 5990
 def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS]
5992 5991
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
5993
-is_a: MS:1000864 ! chemical compound formula
5992
+is_a: MS:1000864 ! chemical formula
5994 5993
 
5995 5994
 [Term]
5996 5995
 id: MS:1000868
5997
-name: SMILES string
5998
-def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [PSI:MS]
5996
+name: SMILES formula
5997
+def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301]
5999 5998
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
6000
-is_a: MS:1000864 ! chemical compound formula
5999
+is_a: MS:1000864 ! chemical formula
6001 6000
 
6002 6001
 [Term]
6003 6002
 id: MS:1000869
... ...
@@ -6086,15 +6085,15 @@ relationship: has_units UO:0000010 ! second
6086 6085
 
6087 6086
 [Term]
6088 6087
 id: MS:1000881
6089
-name: chemical compound
6090
-def: "A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight." [PSI:MS]
6088
+name: molecular entity