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Merge pull request #715 from bigbio/dev
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Major changes in and fixes to all the annotated datasets.
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@ypriverol
ypriverol authored Aug 26, 2024
2 parents 1cd2e2f + af77671 commit 296f3f4
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Showing 25 changed files with 7,638 additions and 7,662 deletions.
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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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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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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