update reference files

HUPO-PSI · Oct 28, 2024 · 3d8c08d · 3d8c08d
1 parent db6bc11
commit 3d8c08d
Show file tree

Hide file tree

Showing 4 changed files with 933 additions and 921 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
@@ -7,19 +7,19 @@ MS:1003207|library creation software=MS:1003253|DIA-NN
 <AttributeSet Interpretation=all>
 <Spectrum=1>
 MS:1003061|library spectrum name=AAAAAAAAAAAAAAAASAGGK2
-MS:1003053|theoretical monoisotopic m/z=778.41296
+MS:1000744|selected ion 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:1000041|charge state=2
 MS:1003059|number of peaks=20
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAAAAAAASAGGK
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAAAAAAASAGGK
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAAAAAAASAGGK/2
 MS:1001117|theoretical mass=1554.8114178831797
-MS:1000041|charge state=2
 [1]MS:1000885|protein accession=P0CG40
 [1]MS:1000886|protein name=SP9_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic
@@ -50,19 +50,19 @@ MS:1000041|charge state=2
 
 <Spectrum=2>
 MS:1003061|library spectrum name=AAAAAAAAAAAAAAAASAGGK3
-MS:1003053|theoretical monoisotopic m/z=519.27777
+MS:1000744|selected ion 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:1000041|charge state=3
 MS:1003059|number of peaks=14
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAAAAAAASAGGK
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAAAAAAASAGGK
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAAAAAAASAGGK/3
 MS:1001117|theoretical mass=1554.8114178831797
-MS:1000041|charge state=3
 [1]MS:1000885|protein accession=P0CG40
 [1]MS:1000886|protein name=SP9_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic
@@ -87,19 +87,19 @@ MS:1000041|charge state=3
 
 <Spectrum=3>
 MS:1003061|library spectrum name=AAAAAAAAAAAAAAAGAGAGAK2
-MS:1003053|theoretical monoisotopic m/z=798.92627
+MS:1000744|selected ion 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:1000041|charge state=2
 MS:1003059|number of peaks=24
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAAAAAAGAGAGAK
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAAAAAAGAGAGAK
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAAAAAAGAGAGAK/2
 MS:1001117|theoretical mass=1595.8379669841897
-MS:1000041|charge state=2
 [1]MS:1000885|protein accession=P55011
 [1]MS:1000886|protein name=S12A2_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic
@@ -134,19 +134,19 @@ MS:1000041|charge state=2
 
 <Spectrum=4>
 MS:1003061|library spectrum name=AAAAAAAAAAAAAAAGAGAGAK3
-MS:1003053|theoretical monoisotopic m/z=532.95325
+MS:1000744|selected ion 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:1000041|charge state=3
 MS:1003059|number of peaks=20
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAAAAAAGAGAGAK
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAAAAAAGAGAGAK
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAAAAAAGAGAGAK/3
 MS:1001117|theoretical mass=1595.8379669841897
-MS:1000041|charge state=3
 [1]MS:1000885|protein accession=P55011
 [1]MS:1000886|protein name=S12A2_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic
@@ -177,19 +177,19 @@ MS:1000041|charge state=3
 
 <Spectrum=5>
 MS:1003061|library spectrum name=AAAAAAAAAAAAAAASGFAYPGTSER3
-MS:1003053|theoretical monoisotopic m/z=746.36969
+MS:1000744|selected ion 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:1000041|charge state=3
 MS:1003059|number of peaks=13
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAAAAAASGFAYPGTSER
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAAAAAASGFAYPGTSER
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAAAAAASGFAYPGTSER/3
 MS:1001117|theoretical mass=2236.087258363109
-MS:1000041|charge state=3
 [1]MS:1000885|protein accession=P35453
 [1]MS:1000886|protein name=HXD13_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic
@@ -213,19 +213,19 @@ MS:1000041|charge state=3
 
 <Spectrum=6>
 MS:1003061|library spectrum name=AAAAAAAAAAAAAAASGFAYPGTSER4
-MS:1003053|theoretical monoisotopic m/z=560.02911
+MS:1000744|selected ion 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:1000041|charge state=4
 MS:1003059|number of peaks=11
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAAAAAASGFAYPGTSER
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAAAAAASGFAYPGTSER
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAAAAAASGFAYPGTSER/4
 MS:1001117|theoretical mass=2236.087258363109
-MS:1000041|charge state=4
 [1]MS:1000885|protein accession=P35453
 [1]MS:1000886|protein name=HXD13_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic
@@ -247,19 +247,19 @@ MS:1000041|charge state=4
 
 <Spectrum=7>
 MS:1003061|library spectrum name=AAAAAAAAAAK2
-MS:1003053|theoretical monoisotopic m/z=429.24561
+MS:1000744|selected ion 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:1000041|charge state=2
 MS:1003059|number of peaks=10
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAK
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAK
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAK/2
 MS:1001117|theoretical mass=856.4766655447999
-MS:1000041|charge state=2
 [1]MS:1000885|protein accession=P50914,P50458,A6NHT5,P15502,DECOY_Q9Y651,DECOY_O60341
 [2]MS:1003275|other attribute name=Proteotypic
 [2]MS:1003276|other attribute value=1
@@ -279,19 +279,19 @@ MS:1000041|charge state=2
 
 <Spectrum=8>
 MS:1003061|library spectrum name=AAAAAAAAAAR2
-MS:1003053|theoretical monoisotopic m/z=443.24869
+MS:1000744|selected ion 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:1000041|charge state=2
 MS:1003059|number of peaks=9
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAAR
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAAR
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAAR/2
 MS:1001117|theoretical mass=884.4828135543999
-MS:1000041|charge state=2
 [1]MS:1000885|protein accession=P47928,Q9Y651,DECOY_Q76L83,DECOY_Q8WXD9,DECOY_Q5VZB9,DECOY_P35453,DECOY_O14654,DECOY_P55011,DECOY_P0CG40
 [2]MS:1003275|other attribute name=Proteotypic
 [2]MS:1003276|other attribute value=1
@@ -310,19 +310,19 @@ MS:1000041|charge state=2
 
 <Spectrum=9>
 MS:1003061|library spectrum name=AAAAAAAAAASGAAIPPLIPPR2
-MS:1003053|theoretical monoisotopic m/z=950.04419
+MS:1000744|selected ion 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:1000041|charge state=2
 MS:1003059|number of peaks=25
 [1]MS:1003275|other attribute name=ExcludeFromAssay
 [1]MS:1003276|other attribute value=False
 <Analyte=1>
 MS:1000888|stripped peptide sequence=AAAAAAAAAASGAAIPPLIPPR
-MS:1003169|proforma peptidoform sequence=AAAAAAAAAASGAAIPPLIPPR
+MS:1003270|proforma peptidoform ion notation=AAAAAAAAAASGAAIPPLIPPR/2
 MS:1001117|theoretical mass=1898.0737805754497
-MS:1000041|charge state=2
 [1]MS:1000885|protein accession=O14654
 [1]MS:1000886|protein name=IRS4_HUMAN
 [2]MS:1003275|other attribute name=Proteotypic