@@ -133,7 +133,8 @@ setMethod("writeMSData", signature(object = "list", file = "character"),

               ## Check software_processing:

               software_processing <- .check_software_processing(software_processing)

               ## Add mzR processing:

-              mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:-1")

+              mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."),

+                       "MS:1002869")

               if (outformat == "mzml")

                   mzR <- c(mzR, "MS:1000544")

               if (outformat == "mzxml")

@@ -178,7 +179,7 @@ copyWriteMSData <- function(object, file, original_file, header,

     ## Check software_processing:

     software_processing <- .check_software_processing(software_processing)

     ## Add mzR processing:

-    mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:-1")

+    mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:1002869")

     if (outformat == "mzml")

         mzR <- c(mzR, "MS:1000544")

     if (outformat == "mzxml")

@@ -1524,6 +1524,9 @@ const TermInfo termInfos_[] =

     {MS_SpectrumMill_Discriminant_Score, "MS:1001580", "SpectrumMill:Discriminant Score", "Discriminant score from Agilent SpectrumMill software.", false},

     {MS_FAIMS_compensation_voltage, "MS:1001581", "FAIMS compensation voltage", "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.", false},

     {MS_XCMS, "MS:1001582", "XCMS", "Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data.", false},

+    {MS_mzR, "MS:1002869", "mzR", "Bioconductor package mzR for reading and writing mass spectrometry data files.", false},

+    {MS_MSnbase, "MS:1002870", "MSnbase", "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.", false},

+    {MS_CAMERA, "MS:1002871", "CAMERA", "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.", false},

     {MS_MaxQuant, "MS:1001583", "MaxQuant", "MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.", false},

     {MS_combined_pmf___ms_ms_search, "MS:1001584", "combined pmf + ms-ms search", "Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF).", false},

     {MS_MyriMatch, "MS:1001585", "MyriMatch", "Tabb Lab software for directly comparing peptides in a database to tandem mass spectra.", false},

@@ -21521,7 +21524,7 @@ class CVTermData : public boost::singleton<CVTermData>

         cvMap_["UNIMOD"].URI = "http://www.unimod.org/obo/unimod.obo";

         cvMap_["MS"].id = "MS";

-        cvMap_["MS"].version = "4.0.1";

+        cvMap_["MS"].version = "4.1.2";

         cvMap_["UNIMOD"].id = "UNIMOD";

         cvMap_["UNIMOD"].version = "2016-07-01";

@@ -8415,6 +8415,15 @@ enum PWIZ_API_DECL CVID

     /// protein group-level result list statistic: Attrbiute of an entire list of protein groups.

     MS_protein_group_level_result_list_statistic = 1002706,

+    /// mzR: Bioconductor package mzR for reading and writing mass spectrometry data files.

+    MS_mzR = 1002869,

+      

+    /// MSnbase: Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data

+    MS_MSnbase = 1002870,

+      

+    /// CAMERA: Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.

+    MS_CAMERA = 1002871,

+      

     /// unimod root node: The root node of the unimod modifications ontology.

     UNIMOD_unimod_root_node = 100000000,