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Major changes in and fixes to all the annotated datasets. #715

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merged 9 commits into from
Aug 26, 2024
Merged

Major changes in and fixes to all the annotated datasets. #715

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7d9e664
readthedocs removed
ypriverol Aug 26, 2024
1f6d527
remove regular expressions for enzymes.
ypriverol Aug 26, 2024
ea92075
remove spaces in modifications
ypriverol Aug 26, 2024
662be2a
more fixes to datasets
ypriverol Aug 26, 2024
cc4ac6e
more fixes to datasets
ypriverol Aug 26, 2024
3993930
more fixes to datasets
ypriverol Aug 26, 2024
6e6825f
more fixes to datasets
ypriverol Aug 26, 2024
dbb9994
more fixes to datasets
ypriverol Aug 26, 2024
af77671
more fixes to datasets
ypriverol Aug 26, 2024
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25 changes: 0 additions & 25 deletions .readthedocs.yaml
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352 changes: 176 additions & 176 deletions annotated-projects/MSV000078555/MSV000078555.sdrf.tsv
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142 changes: 71 additions & 71 deletions annotated-projects/MSV000080451/MSV000080451.sdrf.tsv
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1,100 changes: 550 additions & 550 deletions annotated-projects/PMID33212010/PMID33212010.sdrf.tsv
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540 changes: 270 additions & 270 deletions annotated-projects/PXD000228/PXD000228.sdrf.tsv
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76 changes: 38 additions & 38 deletions annotated-projects/PXD002171/PXD002171.sdrf.tsv
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554 changes: 277 additions & 277 deletions annotated-projects/PXD002192/PXD002192.sdrf.tsv
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766 changes: 383 additions & 383 deletions annotated-projects/PXD003469/PXD003469.sdrf.tsv
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2,580 changes: 1,290 additions & 1,290 deletions annotated-projects/PXD004242/PXD004242.sdrf.tsv
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24 changes: 12 additions & 12 deletions annotated-projects/PXD005241/PXD005241.sdrf.tsv
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36 changes: 18 additions & 18 deletions annotated-projects/PXD005507/PXD005507.sdrf.tsv
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286 changes: 143 additions & 143 deletions annotated-projects/PXD005554/PXD005554.sdrf.tsv
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2,692 changes: 1,346 additions & 1,346 deletions annotated-projects/PXD006003/PXD006003.sdrf.tsv
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40 changes: 20 additions & 20 deletions annotated-projects/PXD009203/PXD009203.sdrf.tsv
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26 changes: 13 additions & 13 deletions annotated-projects/PXD009909/PXD009909.sdrf.tsv
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
source name assay name characteristics[organism] characteristics[organism part] characteristics[cell type] comment[age] characteristics[ancestry category] characteristics[sex] characteristics[disease] characteristics[developmental stage] characteristics[biological replicate] comment[proteomexchange accession number] comment[data file] comment[file uri] comment[fraction identifier] comment[instrument] comment[modification parameters] comment[modification parameters] comment[cleavage agent details] comment[label] comment[fragment mass tolerance] comment[precursor mass tolerance] comment[technical replicate]
Sample 1 run 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_01.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_01.raw 1 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 2 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_02.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_02.raw 2 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 3 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_03.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_03.raw 3 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 4 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_04.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_04.raw 4 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 5 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_05.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_05.raw 5 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 6 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_06.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_06.raw 6 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 7 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_07.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_07.raw 7 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 8 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_08.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_08.raw 8 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 9 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_09.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_09.raw 9 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 10 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_10.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_10.raw 10 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 11 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_11.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_11.raw 11 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 run 12 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 PXD009909 70JG_12.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_12.raw 12 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
source name characteristics[organism] characteristics[organism part] characteristics[cell type] comment[age] characteristics[ancestry category] characteristics[sex] characteristics[disease] characteristics[developmental stage] characteristics[biological replicate] assay name comment[proteomexchange accession number] comment[data file] comment[file uri] comment[fraction identifier] comment[instrument] comment[modification parameters] comment[modification parameters] comment[cleavage agent details] comment[label] comment[fragment mass tolerance] comment[precursor mass tolerance] comment[technical replicate]
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 1 PXD009909 70JG_01.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_01.raw 1 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 2 PXD009909 70JG_02.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_02.raw 2 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 3 PXD009909 70JG_03.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_03.raw 3 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 4 PXD009909 70JG_04.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_04.raw 4 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 5 PXD009909 70JG_05.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_05.raw 5 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 6 PXD009909 70JG_06.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_06.raw 6 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 7 PXD009909 70JG_07.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_07.raw 7 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 8 PXD009909 70JG_08.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_08.raw 8 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 9 PXD009909 70JG_09.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_09.raw 9 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 10 PXD009909 70JG_10.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_10.raw 10 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 11 PXD009909 70JG_11.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_11.raw 11 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
Sample 1 mus musculus Retina not applicable 30 weeks not applicable not available Normal not applicable 1 run 12 PXD009909 70JG_12.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD009909/70JG_12.raw 12 AC=MS:1000639;NT=Orbitrap Fusion NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 AC=MS:1001251;NT=Trypsin label free 0.6 Da 10 ppm 1
6 changes: 3 additions & 3 deletions annotated-projects/PXD010705/PXD010705.sdrf.tsv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[ancestry category] characteristics[age] characteristics[sex] characteristics[disease] characteristics[biological replicate] characteristics[individual] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[associated file uri] comment[label] comment[instrument] comment[cleavage agent details] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[modification parameters] comment[modification parameters]
Sample 1 Homo sapiens Cerebrospinal fluid (CSF) not applicable not available 40Y-85Y not available hydrocephalus 1 not available replicate1 proteomic profiling by mass spectrometry DIA replicate1.raw 1 1 https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD010705/DIA%20replicate1.raw AC=MS:1002038;NT=label free sample NT=Q Exactive; AC = MS:1001911 NT=Trypsin;AC=MS:1001251; CS=(?⇐[KR])(?!P) 5 ppm 20 mmu NT= Carbamidomethyl; MT=variable; PP=Anywhere;AC=Unimod:4; TA=.; MM=57 NT=Oxidation; MT=variable; PP=Anywhere;AC=Unimod:35; TA=M; MM=15.994915
Sample 1 Homo sapiens Cerebrospinal fluid (CSF) not applicable not available 40Y-85Y not available hydrocephalus 1 not available replicate2 proteomic profiling by mass spectrometry DIA replicate2.raw 1 1 https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD010705/DIA%20replicate2.raw AC=MS:1002038;NT=label free sample NT=Q Exactive; AC = MS:1001911 NT=Trypsin;AC=MS:1001251; CS=(?⇐[KR])(?!P) 5 ppm 20 mmu NT= Carbamidomethyl; MT=variable; PP=Anywhere;AC=Unimod:4; TA=.; MM=57 NT=Oxidation; MT=variable; PP=Anywhere;AC=Unimod:35; TA=M; MM=15.994915
Sample 1 Homo sapiens Cerebrospinal fluid (CSF) not applicable not available 40Y-85Y not available hydrocephalus 1 not available replicate3 proteomic profiling by mass spectrometry DIA replicate3.raw 1 1 https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD010705/DIA%20replicate3.raw AC=MS:1002038;NT=label free sample NT=Q Exactive; AC = MS:1001911 NT=Trypsin;AC=MS:1001251; CS=(?⇐[KR])(?!P) 5 ppm 20 mmu NT= Carbamidomethyl; MT=variable; PP=Anywhere;AC=Unimod:4; TA=.; MM=57 NT=Oxidation; MT=variable; PP=Anywhere;AC=Unimod:35; TA=M; MM=15.994915
Sample 1 Homo sapiens Cerebrospinal fluid (CSF) not applicable not available 40Y-85Y not available hydrocephalus 1 not available replicate1 proteomic profiling by mass spectrometry DIA replicate1.raw 1 1 https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD010705/DIA%20replicate1.raw AC=MS:1002038;NT=label free sample NT=Q Exactive; AC = MS:1001911 NT=Trypsin;AC=MS:1001251 5 ppm 20 mmu NT= Carbamidomethyl; MT=variable; PP=Anywhere;AC=Unimod:4; TA=.; MM=57 NT=Oxidation; MT=variable; PP=Anywhere;AC=Unimod:35; TA=M; MM=15.994915
Sample 1 Homo sapiens Cerebrospinal fluid (CSF) not applicable not available 40Y-85Y not available hydrocephalus 1 not available replicate2 proteomic profiling by mass spectrometry DIA replicate2.raw 1 1 https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD010705/DIA%20replicate2.raw AC=MS:1002038;NT=label free sample NT=Q Exactive; AC = MS:1001911 NT=Trypsin;AC=MS:1001251 5 ppm 20 mmu NT= Carbamidomethyl; MT=variable; PP=Anywhere;AC=Unimod:4; TA=.; MM=57 NT=Oxidation; MT=variable; PP=Anywhere;AC=Unimod:35; TA=M; MM=15.994915
Sample 1 Homo sapiens Cerebrospinal fluid (CSF) not applicable not available 40Y-85Y not available hydrocephalus 1 not available replicate3 proteomic profiling by mass spectrometry DIA replicate3.raw 1 1 https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/09/PXD010705/DIA%20replicate3.raw AC=MS:1002038;NT=label free sample NT=Q Exactive; AC = MS:1001911 NT=Trypsin;AC=MS:1001251 5 ppm 20 mmu NT= Carbamidomethyl; MT=variable; PP=Anywhere;AC=Unimod:4; TA=.; MM=57 NT=Oxidation; MT=variable; PP=Anywhere;AC=Unimod:35; TA=M; MM=15.994915
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