@@ -2,7 +2,7 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.11.4

+Version: 2.11.5

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,

 	    Steffen Neumann <sneumann@ipb-halle.de>,

@@ -1,7 +1,10 @@

 CHANGES IN VERSION 2.11.4

 -------------------------

- o writeMSData and copyWriteMSData functions enabling to export MS data to

-   mzML or mzXML files.

+ o Nothing yet

+ 

+CHANGES IN VERSION 2.11.4

+-------------------------

+ o Use full TMT file pattern to select a single file

 CHANGES IN VERSION 2.11.3

 -------------------------

@@ -14,7 +14,8 @@ test_chromatograms1 <- function() {

 }

 test_chromatograms2 <- function() {

-    f <- proteomics(full.names = TRUE, pattern = "^TMT")

+    f <- proteomics(full.names = TRUE,

+                    pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

     x <- openMSfile(f, backend = "pwiz")

     checkIdentical(nChrom(x), 1L)   

     checkIdentical(tic(x), chromatogram(x, 1L))

@@ -1,6 +1,7 @@

 test_isolationWindow <- function() {

     library("msdata")

-    f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_")

+    f <- msdata::proteomics(full.names = TRUE,

+                            pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

     rw1 <- openMSfile(f, backend = "Ramp")

     rw2 <- openMSfile(f, backend = "pwiz")

     i1 <- isolationWindow(f)

@@ -118,7 +118,8 @@ test_getScanHeaderInfo <- function() {

     close(ramp)

     ## Again for an MSn mzml file.

-    file <- msdata::proteomics(full.names = TRUE, pattern = "TMT_Erwinia")

+    file <- msdata::proteomics(full.names = TRUE,

+                               pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

     mzml <- openMSfile(file, backend = "pwiz")

     ramp <- openMSfile(file, backend = "Ramp")

     ## Read single scan header.

@@ -51,7 +51,8 @@

 \examples{

 library("msdata")

-f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_")

+f <- msdata::proteomics(full.names = TRUE,

+                        pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

 isolationWindow(f)

 rw <- openMSfile(f)

@@ -151,7 +151,8 @@

  close(mz)

  ## A shortgun LCMSMS experiment 

- f <- proteomics(full.names = TRUE, pattern = "^TMT")

+ f <- proteomics(full.names = TRUE,

+                 pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

  x <- openMSfile(f, backend = "pwiz")

  x

  nChrom(x)