Skip to content

Commit a13d90c

Browse files
ypriverolclaude
ypriverol
and
claude
committed
fix: Fix data issues in SDRF files (Phase 2)
- Replace 'not applicable' with '1' in comment[fraction identifier] (300 cells) - Remove spaces in age values: '30Y 6M' -> '30Y6M' (20 cells) - Move 'adult' from characteristics[age] to characteristics[developmental stage] (136 cells) Files modified: 12 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
1 parent 8546925 commit a13d90c

13 files changed

Lines changed: 599 additions & 461 deletions

File tree

‎annotated-projects/MSV000078494/MSV000078494.sdrf.tsv‎

Lines changed: 8 additions & 8 deletions
Large diffs are not rendered by default.

‎annotated-projects/PXD000815/PXD000815.sdrf.tsv‎

Lines changed: 20 additions & 20 deletions
Large diffs are not rendered by default.

‎annotated-projects/PXD002395/PXD002395.sdrf.tsv‎

Lines changed: 18 additions & 18 deletions
Large diffs are not rendered by default.

‎annotated-projects/PXD003133/PXD003133.sdrf.tsv‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
source name characteristics[organism] characteristics[organism part] characteristics[age] characteristics[sex] characteristics[ancestry category] characteristics[cell type] characteristics[individual] characteristics[cell line] characteristics[disease] characteristics[developmental stage] characteristics[biological replicate] characteristics[material type] assay name technology type comment[proteomics data acquisition method] comment[data file] comment[file uri] comment[technical replicate] comment[fraction identifier] comment[instrument] comment[cleavage agent details] comment[label] comment[modification parameters] comment[fragment mass tolerance] comment[precursor mass tolerance] comment[sdrf version] comment[sdrf template]
2-
Sample 1 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 1 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140522_1.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140323_1.raw 1 not applicable AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
3-
Sample 2 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 2 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140521_2.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140521_1.raw 1 not applicable AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
4-
Sample 3 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 3 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140521_1.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140521_2.raw 1 not applicable AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
5-
Sample 4 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 4 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140323_1.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140522_1.raw 1 not applicable AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
2+
Sample 1 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 1 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140522_1.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140323_1.raw 1 1 AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
3+
Sample 2 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 2 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140521_2.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140521_1.raw 1 1 AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
4+
Sample 3 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 3 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140521_1.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140521_2.raw 1 1 AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0
5+
Sample 4 Homo sapiens kidney not available not available not applicable not applicable not applicable HEK293 not available not available 1 cell run 4 proteomic profiling by mass spectrometry NT=Data-dependent acquisition;AC=PRIDE:0000627 QC_20140323_1.raw https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/QC_20140522_1.raw 1 1 AC=MS:1001742;NT=LTQ Orbitrap Velos AC=MS:1001251;NT=Trypsin AC=MS:1002038;NT=label free sample not available 0.5 Da 20 ppm v1.1.0 NT=ms-proteomics;version=v1.1.0

‎annotated-projects/PXD003539/PXD003539.sdrf.tsv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[cell line] characteristics[developmental stage] characteristics[disease] characteristics[ancestry category] characteristics[sex] characteristics[age] characteristics[material type] characteristics[biological replicate] assay name technology type comment[proteomics data acquisition method] comment[data file] comment[file uri] comment[proteomexchange accession number] comment[technical replicate] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument] comment[modification parameters] comment[modification parameters].1 comment[lowest observed m/z] comment[highest observed m/z] comment[sdrf version] comment[sdrf template] factor value[cell line]
2-
LE_CCRFCEM_a Homo sapiens blood not available CCRFCEM not available acute lymphoblastic leukemia caucasian Female 3Y 11M cell 1 Run 1 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130610_003_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130610_003_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 CCRFCEM
2+
LE_CCRFCEM_a Homo sapiens blood not available CCRFCEM not available acute lymphoblastic leukemia caucasian Female 3Y11M cell 1 Run 1 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130610_003_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130610_003_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 CCRFCEM
33
LC_EKVX_a Homo sapiens lung not available EKVX not available non-small cell lung carcinoma caucasian Male not available cell 1 Run 2 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130610_004_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130610_004_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 EKVX
44
CO_HCT116_a Homo sapiens large intestine not available HCT116 not available colon carcinoma caucasian Male 48Y cell 1 Run 3 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130610_005_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130610_005_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 HCT116
55
OV_IGROV1_a Homo sapiens ovary not available IGROV-1 not available ovarian carcinoma caucasian Female 47Y cell 1 Run 4 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130610_006_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130610_006_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 IGROV-1
@@ -56,7 +56,7 @@ LC_HOP92_a Homo sapiens lung not available HOP-92 not available large cell lung
5656
ME_LOXIMVI_a Homo sapiens skin not available LOX IMVI not available skin cutaneous melanoma caucasian Male 58Y cell 1 Run 55 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130621_003_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130621_003_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 LOX IMVI
5757
PR_PC3_a Homo sapiens prostate not available PC-3 not available prostate adenocarcinoma caucasian Male 62Y cell 1 Run 56 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130621_004_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130621_004_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 PC-3
5858
RE_SN12C_a Homo sapiens kidney not available SN12C not available renal cell carcinoma caucasian Male not available cell 1 Run 57 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130621_005_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130621_005_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 SN12C
59-
LE_CCRFCEM_b Homo sapiens blood not available CCRFCEM not available acute lymphoblastic leukemia caucasian Female 3Y 11M cell 2 Run 58 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130622_002_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130622_002_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 CCRFCEM
59+
LE_CCRFCEM_b Homo sapiens blood not available CCRFCEM not available acute lymphoblastic leukemia caucasian Female 3Y11M cell 2 Run 58 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130622_002_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130622_002_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 CCRFCEM
6060
LC_EKVX_b Homo sapiens lung not available EKVX not available non-small cell lung carcinoma caucasian Male not available cell 2 Run 59 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130622_003_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130622_003_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 EKVX
6161
CO_HCT116_b Homo sapiens large intestine not available HCT116 not available colon carcinoma caucasian Male 48Y cell 2 Run 60 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130622_004_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130622_004_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 HCT116
6262
OV_IGROV1_b Homo sapiens ovary not available IGROV-1 not available ovarian carcinoma caucasian Female 47Y cell 2 Run 61 proteomic profiling by mass spectrometry data-dependent acquisition guot_L130622_005_SW.wiff https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD003539/guot_L130622_005_SW.wiff PXD003539 1 1 AC=MS:1002038;NT=label free sample AC=MS:1001251;NT=Trypsin NT=TripleTOF 5600;AC=MS:1000932 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 NT=Oxidation;MT=Variable;TA=M;AC=UNIMOD:35 400 1200 v1.1.0 NT=ms-proteomics;version=v1.1.0 IGROV-1

0 commit comments

Comments
 (0)