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56305e4
lower reserved words
wouter-l Mar 31, 2026
e41b07f
add name to contributor list
wouter-l Mar 31, 2026
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -114,6 +114,7 @@ The project is run by different groups:
- Deepti Jaiswal Kundu (PRIDE Team, European Bioinformatics Institute - EMBL-EBI, U.K.)
- Nandana Madhusoodanan (PRIDE Team, European Bioinformatics Institute - EMBL-EBI, U.K.)
- Diogo Borges Lima (Exact Sciences Corp., Munich, Germany)
- Wouter Lampaert (Brussels, Belgium)

IMPORTANT: If you contribute with the following specification, please make sure to add your name to the list of contributors.

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540 changes: 270 additions & 270 deletions annotated-projects/PXD000228/PXD000228.sdrf.tsv
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168 changes: 84 additions & 84 deletions annotated-projects/PXD000498/PXD000498.sdrf.tsv
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272 changes: 136 additions & 136 deletions annotated-projects/PXD007073/PXD007073.sdrf.tsv
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4 changes: 2 additions & 2 deletions annotated-projects/PXD007864/PXD007864.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[strain/breed] characteristics[disease] characteristics[cell type] characteristics[enrichment process] characteristics[biological replicate] characteristics[medium] characteristics[temperature] assay name technology type comment[technical replicate] comment[proteomics data acquisition method] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details] comment[fragment mass tolerance] comment[precursor mass tolerance] comment[reduction reagent] comment[alkylation reagent] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[file uri] comment[sdrf version] comment[sdrf template] factor value[enrichment process]
His IP Escherichia coli Cell lysate Escherichia coli str. K-12 substr. MC4100 Not applicable Prokaryotic cell Affinity purification via anti-His antibody 1 Not available 37°C Run 1 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 His_IP_1_DDA.raw 1 Label free sample NT=Q Exactive NT=Trypsin;AC=1001251 0.02 Da 10 ppm DTT IAA NT=Carbamidomethyl;AC=4;CF=H(3) C(2) N O;MM=57.021464;MT=Fixed;PP=Anywhere;TA=['C'] NT=Oxidation; MT=Variable; TA=M NT=Phospho; MT=Variable; TA=S,T,Y NT=HCD; AC=MS:1002481 https://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD007864/His_IP_1_DDA.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Affinity purification via anti-His antibody
IgG IP Escherichia coli Cell lysate Escherichia coli str. K-12 substr. MC4100 Not applicable Prokaryotic cell Control 1 Not available 37°C Run 2 Proteomic profiling by mass spectrometry 2 NT=Data-dependent acquisition;AC=PRIDE:0000627 IgG_IP_1_DDA.raw 1 Label free sample NT=Q Exactive NT=Trypsin;AC=1001251 0.02 Da 10 ppm DTT IAA NT=Carbamidomethyl;AC=4;CF=H(3) C(2) N O;MM=57.021464;MT=Fixed;PP=Anywhere;TA=['C'] NT=Oxidation; MT=Variable; TA=M NT=Phospho; MT=Variable; TA=S,T,Y NT=HCD; AC=MS:1002481 https://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD007864/IgG_IP_1_DDA.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Control
His IP Escherichia coli Cell lysate Escherichia coli str. K-12 substr. MC4100 not applicable Prokaryotic cell Affinity purification via anti-His antibody 1 not available 37°C Run 1 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 His_IP_1_DDA.raw 1 Label free sample NT=Q Exactive NT=Trypsin;AC=1001251 0.02 Da 10 ppm DTT IAA NT=Carbamidomethyl;AC=4;CF=H(3) C(2) N O;MM=57.021464;MT=Fixed;PP=Anywhere;TA=['C'] NT=Oxidation; MT=Variable; TA=M NT=Phospho; MT=Variable; TA=S,T,Y NT=HCD; AC=MS:1002481 https://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD007864/His_IP_1_DDA.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Affinity purification via anti-His antibody
IgG IP Escherichia coli Cell lysate Escherichia coli str. K-12 substr. MC4100 not applicable Prokaryotic cell Control 1 not available 37°C Run 2 Proteomic profiling by mass spectrometry 2 NT=Data-dependent acquisition;AC=PRIDE:0000627 IgG_IP_1_DDA.raw 1 Label free sample NT=Q Exactive NT=Trypsin;AC=1001251 0.02 Da 10 ppm DTT IAA NT=Carbamidomethyl;AC=4;CF=H(3) C(2) N O;MM=57.021464;MT=Fixed;PP=Anywhere;TA=['C'] NT=Oxidation; MT=Variable; TA=M NT=Phospho; MT=Variable; TA=S,T,Y NT=HCD; AC=MS:1002481 https://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD007864/IgG_IP_1_DDA.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Control
36 changes: 18 additions & 18 deletions annotated-projects/PXD008369/PXD008369.sdrf.tsv
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72 changes: 36 additions & 36 deletions annotated-projects/PXD008921/PXD008921.sdrf.tsv
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64 changes: 32 additions & 32 deletions annotated-projects/PXD011023/PXD011023.sdrf.tsv
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68 changes: 34 additions & 34 deletions annotated-projects/PXD012611/PXD012611.sdrf.tsv
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56 changes: 28 additions & 28 deletions annotated-projects/PXD013273/PXD013273.sdrf.tsv
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12 changes: 6 additions & 6 deletions annotated-projects/PXD013610/PXD013610.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[culture type] characteristics[strain/breed] characteristics[disease] characteristics[cell type] characteristics[biological replicate] characteristics[medium] characteristics[temperature] characteristics[growth phase] assay name technology type comment[technical replicate] comment[proteomics data acquisition method] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details] comment[reduction reagent] comment[alkylation reagent] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[file uri] comment[sdrf version] comment[sdrf template] factor value[culture type]
Exponential 1 Escherichia coli Cell lysate Exponential culture Escherichia coli BW35113 Not applicable Prokaryotic cell 1 LB medium 37°C Exponential phase Run 1 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 a0,5t.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/a0,5t.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Exponential culture
Stationary 1 Escherichia coli Cell lysate Stationary culture Escherichia coli BW35113 Not applicable Prokaryotic cell 1 LB medium 37°C Stationary phase Run 2 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 ayt_161207182650.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/ayt_161207182650.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Stationary culture
Exponential 2 Escherichia coli Cell lysate Exponential culture Escherichia coli BW35113 Not applicable Prokaryotic cell 2 LB medium 37°C Exponential phase Run 3 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 b0,5t.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/b0,5t.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Exponential culture
Stationary 2 Escherichia coli Cell lysate Stationary culture Escherichia coli BW35113 Not applicable Prokaryotic cell 2 LB medium 37°C Stationary phase Run 4 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 byt_161207194536.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/byt_161207194536.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Stationary culture
Exponential 3 Escherichia coli Cell lysate Exponential culture Escherichia coli BW35113 Not applicable Prokaryotic cell 3 LB medium 37°C Exponential phase Run 5 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 c0,5t.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/c0,5t.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Exponential culture
Stationary 3 Escherichia coli Cell lysate Stationary culture Escherichia coli BW35113 Not applicable Prokaryotic cell 3 LB medium 37°C Stationary phase Run 6 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 cyt.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/cyt.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Stationary culture
Exponential 1 Escherichia coli Cell lysate Exponential culture Escherichia coli BW35113 not applicable Prokaryotic cell 1 LB medium 37°C Exponential phase Run 1 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 a0,5t.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/a0,5t.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Exponential culture
Stationary 1 Escherichia coli Cell lysate Stationary culture Escherichia coli BW35113 not applicable Prokaryotic cell 1 LB medium 37°C Stationary phase Run 2 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 ayt_161207182650.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/ayt_161207182650.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Stationary culture
Exponential 2 Escherichia coli Cell lysate Exponential culture Escherichia coli BW35113 not applicable Prokaryotic cell 2 LB medium 37°C Exponential phase Run 3 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 b0,5t.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/b0,5t.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Exponential culture
Stationary 2 Escherichia coli Cell lysate Stationary culture Escherichia coli BW35113 not applicable Prokaryotic cell 2 LB medium 37°C Stationary phase Run 4 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 byt_161207194536.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/byt_161207194536.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Stationary culture
Exponential 3 Escherichia coli Cell lysate Exponential culture Escherichia coli BW35113 not applicable Prokaryotic cell 3 LB medium 37°C Exponential phase Run 5 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 c0,5t.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/c0,5t.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Exponential culture
Stationary 3 Escherichia coli Cell lysate Stationary culture Escherichia coli BW35113 not applicable Prokaryotic cell 3 LB medium 37°C Stationary phase Run 6 Proteomic profiling by mass spectrometry 1 NT=Data-dependent acquisition;AC=PRIDE:0000627 cyt.raw 1 Label free sample NT=Orbitrap Fusion NT=Trypsin;AC=1001251 TCEP MMTS NT=Methylthio; AC=UNIMOD:39;TA=C NT=Oxidation; MT=Variable; TA=M NT=Acetyl; MT=Variable; PP=Protein N-term NT=HCD; AC=MS:1002481 30% NCE https://ftp.pride.ebi.ac.uk/pride/data/archive/2019/06/PXD013610/cyt.raw v1.1.0 NT=ms-proteomics;VV=v1.1.0 Stationary culture
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