Merge branch 'master' of https://github.com/HUPO-PSI/mzSpecLib

HUPO-PSI · Oct 22, 2024 · db6bc11 · db6bc11
2 parents 29d8786 + 6fb730f
commit db6bc11
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diff --git a/README.md b/README.md
@@ -15,9 +15,11 @@ the developers of spectral library search tools and resources.
 
 ---
 
-- [Introduction](#introduction)
-- [Development](#development)
-- [Contributing](#contributing)
+- [mzSpecLib](#mzspeclib)
+  - [Introduction](#introduction)
+  - [Development](#development)
+  - [Reference implementation](#reference-implementation)
+  - [Contributing](#contributing)
 
 ---
 
@@ -53,12 +55,12 @@ is used as a central point of information regarding the format's development:
   formats, the spectral library controlled vocabulary, the spectral library
   specifications, examples and tools that export/validate and visualize those
   files.
-- Additionally, Google Docs are used to quickly and efficiently collaborate
-  on the specification documents. Links to these documents are listed here:
-  - [mzSpecLib main specification document](https://docs.google.com/document/d/1l87lIyKTy2ti5yU7aqsLr7uX5jIU1dO7gEzyqWD2uQA/edit?usp=sharing)
-  - [Metadata and CV term overview](https://drive.google.com/file/d/1rN5DJSowp2micxlwJQlPxlv39ZiaLEfv/edit?usp=sharing)
-  - [mzSpecLib peak interetation format](https://docs.google.com/document/d/1yEUNG4Ump6vnbMDs4iV4s3XISflmOkRAyqUuutcCG2w/edit?usp=sharing)
-  - [mzSpecLib general data model schematic](https://drive.google.com/file/d/1OVh5ATfKXA77pM4CYzRfdupeRGu3vt5c/view?usp=sharing)
+- The mzSpecLib specification is nearly complete and has been resubmitted to the PSI Document Process for final community review. It is hoped to be complete at the end of 2024.
+
+If you do experience problems with the files or have suggestions or comments, please open an [issue](https://github.com/HUPO-PSI/mzSpecLib/issues).
+
+- [mzSpecLib main specification document](https://github.com/HUPO-PSI/mzSpecLib/blob/master/specification/mzSpecLib_specification_v1.0_draft09.docx)
+- [mzPAF peak interetation format](https://psidev.info/mzPAF)
 
 
 ## Reference implementation

diff --git a/examples/NIST-CPTAC/broad_tcga_nonphospho_consensus_rec.head.mzlb.txt b/examples/NIST-CPTAC/broad_tcga_nonphospho_consensus_rec.head.mzlb.txt
@@ -1,4 +1,4 @@
-<mzSpecLib 1.0>
+<mzSpecLib>
 MS:1003186|library format version=1.0
 MS:1003188|library name=broad_tcga_nonphospho_consensus_rec
 <AttributeSet Spectrum=all>
@@ -30,6 +30,7 @@ MS:1003059|number of peaks=27
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=582.3537
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=582.3537
 <Peaks>
 102.0669	4240.31	4498 4498
 102.5695	187.126	3292 4498
@@ -85,6 +86,7 @@ MS:1003059|number of peaks=27
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=626.3797
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=626.3797
 <Peaks>
 102.0671	4104.76	4197 4197
 102.5695	192.432	3172 4197
@@ -140,6 +142,7 @@ MS:1003059|number of peaks=33
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=505.9752
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=505.9752
 <Peaks>
 102.0678	5317.97	4098 4098
 102.5695	472.994	3878 4098
@@ -201,6 +204,7 @@ MS:1003059|number of peaks=24
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=604.3668
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=604.3668
 <Peaks>
 102.0671	4100.02	3901 3901
 102.5695	171.451	2808 3901
@@ -253,6 +257,7 @@ MS:1003059|number of peaks=34
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=520.6507
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=520.6507
 <Peaks>
 102.0678	5111.57	3890 3890
 102.5695	455.606	3679 3890
@@ -315,6 +320,7 @@ MS:1003059|number of peaks=24
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=560.3406
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=560.3406
 <Peaks>
 102.0671	4256.33	3869 3869
 102.5695	178.328	2710 3869
@@ -367,6 +373,7 @@ MS:1003059|number of peaks=31
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=491.2997
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=491.2997
 <Peaks>
 102.0678	5306.39	3862 3862
 102.5695	450.08	3590 3862
@@ -426,6 +433,7 @@ MS:1003059|number of peaks=26
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=648.3928
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=648.3928
 <Peaks>
 102.0665	4054.14	3775 3775
 102.5695	171.454	2793 3775
@@ -480,6 +488,7 @@ MS:1003059|number of peaks=35
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=511.6505
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=511.6505
 <Peaks>
 102.0678	3928.31	3736 3736
 102.5695	331.903	3450 3736
@@ -543,6 +552,7 @@ MS:1003059|number of peaks=37
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=526.3259
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=526.3259
 <Peaks>
 102.0678	3876.34	3565 3565
 102.5695	324.37	3271 3565
@@ -608,6 +618,7 @@ MS:1003059|number of peaks=27
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=670.4059
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=670.4059
 <Peaks>
 102.0667	3993.59	3503 3503
 102.5695	179.953	2654 3503
@@ -663,6 +674,7 @@ MS:1003059|number of peaks=36
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=541.0012
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=541.0012
 <Peaks>
 102.0671	3820.57	3502 3502
 102.5695	304.378	3176 3502
@@ -727,6 +739,7 @@ MS:1003059|number of peaks=42
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=535.326
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=535.326
 <Peaks>
 102.0678	5369.89	3443 3443
 102.5695	465.348	3252 3443
@@ -797,6 +810,7 @@ MS:1003059|number of peaks=23
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=494.3013
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=494.3013
 <Peaks>
 102.0671	4594.8	3240 3240
 102.5695	225.127	2412 3240
@@ -848,6 +862,7 @@ MS:1003059|number of peaks=30
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=568.8535
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=568.8535
 <Peaks>
 102.0667	2457.31	3179 3179
 102.5695	65.9208	1847 3179
@@ -906,6 +921,7 @@ MS:1003059|number of peaks=26
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=538.3277
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=538.3277
 <Peaks>
 102.0673	4467.51	3154 3154
 102.5695	206.325	2275 3154
@@ -960,6 +976,7 @@ MS:1003059|number of peaks=33
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=564.6766
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=564.6766
 <Peaks>
 102.0673	4963.19	3124 3124
 102.5695	420.454	2920 3124
@@ -1021,6 +1038,7 @@ MS:1003059|number of peaks=38
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=496.9749
 MS:1000041|charge state=3
+MS:1000744|selected ion m/z=496.9749
 <Peaks>
 102.0669	4116.19	3091 3091
 102.5695	331.44	2784 3091
@@ -1087,6 +1105,7 @@ MS:1003059|number of peaks=33
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=612.8796
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=612.8796
 <Peaks>
 102.0665	2352.81	3080 3080
 102.5695	57.178	1731 3080
@@ -1148,6 +1167,7 @@ MS:1003059|number of peaks=29
 [8]MS:1003276|other attribute value="Nov 14 2014"
 MS:1003208|experimental precursor monoisotopic m/z=692.4188
 MS:1000041|charge state=2
+MS:1000744|selected ion m/z=692.4188
 <Peaks>
 102.067	3878.14	3078 3078
 102.5695	162.683	2257 3078

diff --git a/specification/README.md b/specification/README.md
@@ -1,10 +1,8 @@
 # mzSpecLib specification
 
-The mzSpecLib specification is mainly being developed using Google Docs. With the following links you can add comments and suggest changes to the specification. All input is welcome!
+The mzSpecLib specification is nearly complete and has been resubmitted to the PSI Document Process for final community review. It is hoped to be complete at the end of 2024.
 
-If you do experience problems to open or edit the files, please open an [issue](https://github.com/HUPO-PSI/mzSpecLib/issues).
+If you do experience problems with the files or have suggestions or comments, please open an [issue](https://github.com/HUPO-PSI/mzSpecLib/issues).
 
-- [mzSpecLib main specification document](https://docs.google.com/document/d/1l87lIyKTy2ti5yU7aqsLr7uX5jIU1dO7gEzyqWD2uQA/edit?usp=sharing)
-- [Metadata and CV term overview](https://drive.google.com/file/d/1rN5DJSowp2micxlwJQlPxlv39ZiaLEfv/edit?usp=sharing)
-- [mzSpecLib peak interetation format](https://docs.google.com/document/d/1yEUNG4Ump6vnbMDs4iV4s3XISflmOkRAyqUuutcCG2w/edit?usp=sharing)
-- [mzSpecLib general data model schematic](https://drive.google.com/file/d/1OVh5ATfKXA77pM4CYzRfdupeRGu3vt5c/view?usp=sharing)
+- [mzSpecLib main specification document](https://github.com/HUPO-PSI/mzSpecLib/blob/master/specification/mzSpecLib_specification_v1.0_draft09.docx)
+- [mzPAF peak interetation format](https://psidev.info/mzPAF)
diff --git a/specification/mzSpecLib_specification_v1.0-draft5.docx b/specification/mzSpecLib_specification_v1.0-draft5.docx
diff --git a/specification/mzSpecLib_specification_v1.0_draft09.docx b/specification/mzSpecLib_specification_v1.0_draft09.docx