Update library files (#85)

* Update library files * fix spice library
HUPO-PSI · Sep 13, 2024 · aacdb9c · aacdb9c
1 parent 1e5ce4a
commit aacdb9c
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Showing 8 changed files with 2,388 additions and 1,866 deletions.
diff --git a/examples/DIA-NN/phl004_canonical_sall_pv_plasma.head.diann.mzlib.txt b/examples/DIA-NN/phl004_canonical_sall_pv_plasma.head.diann.mzlib.txt
@@ -1,4 +1,4 @@
-<mzSpecLib 1.0>
+<mzSpecLib>
 MS:1003186|library format version=1.0
 MS:1003188|library name=phl004_canonical_sall_pv_plasma.head.diann
 MS:1003207|library creation software=MS:1003253|DIA-NN
@@ -10,6 +10,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAAAAAAASAGGK2
 MS:1003053|theoretical monoisotopic m/z=778.41296
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=20
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -52,6 +53,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAAAAAAASAGGK3
 MS:1003053|theoretical monoisotopic m/z=519.27777
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=14
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -88,6 +90,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAAAAAAGAGAGAK2
 MS:1003053|theoretical monoisotopic m/z=798.92627
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=24
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -134,6 +137,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAAAAAAGAGAGAK3
 MS:1003053|theoretical monoisotopic m/z=532.95325
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=20
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -176,6 +180,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAAAAAASGFAYPGTSER3
 MS:1003053|theoretical monoisotopic m/z=746.36969
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=13
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -211,6 +216,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAAAAAASGFAYPGTSER4
 MS:1003053|theoretical monoisotopic m/z=560.02911
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=11
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -244,6 +250,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAK2
 MS:1003053|theoretical monoisotopic m/z=429.24561
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=10
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -275,6 +282,7 @@ MS:1003061|library spectrum name=AAAAAAAAAAR2
 MS:1003053|theoretical monoisotopic m/z=443.24869
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=9
 [1]MS:1003275|other attribute name=ExcludeFromAssay
@@ -305,6 +313,7 @@ MS:1003061|library spectrum name=AAAAAAAAAASGAAIPPLIPPR2
 MS:1003053|theoretical monoisotopic m/z=950.04419
 MS:1003203|constituent spectrum file=file:///home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv
 MS:1003072|spectrum origin type=MS:1003074|predicted spectrum
+MS:1003065|spectrum aggregation type=MS:1003074|predicted spectrum
 MS:1002476|ion mobility drift time=0.0
 MS:1003059|number of peaks=25
 [1]MS:1003275|other attribute name=ExcludeFromAssay

diff --git a/examples/NIST/IARPA3_best_tissue_add_info.head.mzlib.txt b/examples/NIST/IARPA3_best_tissue_add_info.head.mzlib.txt
@@ -1,4 +1,4 @@
-<mzSpecLib 1.0>
+<mzSpecLib>
 MS:1003186|library format version=1.0
 MS:1003188|library name=IARPA3_best_tissue_add_info
 MS:1003191|library URI=https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:lib:human_skin_hair

diff --git a/examples/NIST/broad_tcga_nonphospho_consensus_rec.head.mzlb.txt b/examples/NIST/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