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A repository to convert SDRF proteomics files into pipelines config files
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Report error with validate SDRF if factor value column doesn't correspond to characteristics column #167

Closed kai-lawsonmcdowall closed 6 days ago

kai-lawsonmcdowall commented 2 months ago

To my understanding, a factor value column should have a corresponding characteristics column. However, when I run the parse_sdrf validate-sdrf command, despite having a factor value column which has no corresponding characteristics column, no error is thrown. Ideally, an error should be thrown to alert the user that the factor value column they have created has no corresponding characteristics column.

ypriverol commented 2 months ago

Thanks @kai-lawsonmcdowall for reporting the bug. We will take care of it. Do you think you could help us (contribute) on fixing it?

kai-lawsonmcdowall commented 2 months ago

Hi Yasset,

I think it should be conceptually pretty simple, I can certainly give it a go!

ypriverol commented 2 months ago

Hi Yasset,

I think it should be conceptually pretty simple, I can certainly give it a go!

🥳

kai-lawsonmcdowall commented 2 months ago

Hi Yasset, took a quick look at the code, Maybe I'm wrong, but it looks like there's already the function in sdrf_schema.py, the validate_column_names method in the class SDRFSchema is checking factor value against characteristic. However, it's not being called as far as I can tell in in the validate_sdrf function when parse_sdrf is run.

I admit I haven't figured out the code ecosystem yet, but as far as I can tell this is what's causing the lack of checking between the characteristics and the factor_value columns

ypriverol commented 2 months ago

I will take a look today @kai-lawsonmcdowall. We have been thinking for a while about refactoring a little the code to move into pydantic; but we haven't found the time to do it. I will check today and ping you when Im done.

ypriverol commented 2 weeks ago

@kai-lawsonmcdowall do you have an example for this issue? I got some time to double-check the code.

kai-lawsonmcdowall commented 2 weeks ago

Hi Yasset, sure thing, can't upload the sdrf.tsv to github, I've attached in a code block here, this was modification of an sdrf from a PRIDE project PXD000312 which I modified, there is the factor value[concentration of] column but no characteristics[concentration of] column. On my end this passed when I ran parse_sdrf validate-sdrf -s PXD000312_issue_167.sdrf.csv

source name characteristics[organism]   characteristics[organism part]  characteristics[cell type]  characteristics[developmental stage]    characteristics[disease]    characteristics[enrichment process] characteristics[biological replicate]   characteristics[compound]   characteristics[cell line]  assay name  technology type comment[data file]  comment[technical replicate]    comment[fraction identifier]    comment[label]  comment[cleavage agent details] comment[modification parameters]    comment[modification parameters]    comment[modification parameters]    comment[modification parameters]    comment[instrument] comment[associated file uri]    factor value[compound]  factor value[concentration of]

E1S1    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 1   proteomic profiling by mass spectrometry    1342_01.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_01.RAW   none    not applicable
E1S2    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 2   proteomic profiling by mass spectrometry    1342_02.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_02.RAW   none    not applicable
E1S3    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 3   proteomic profiling by mass spectrometry    1342_03.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_03.RAW   none    not applicable
E1S4    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 4   proteomic profiling by mass spectrometry    1342_04.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_04.RAW   none    not applicable
E1S5    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 5   proteomic profiling by mass spectrometry    1342_05.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_05.RAW   mercury dichloride  250 uM
E1S6    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 6   proteomic profiling by mass spectrometry    1342_06.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_06.RAW   mercury dichloride  250 uM
E1S7    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 7   proteomic profiling by mass spectrometry    1342_07.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_07.RAW   mercury dichloride  250 uM
E1S8    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 8   proteomic profiling by mass spectrometry    1342_08.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_08.RAW   mercury dichloride  250 uM
E1S9    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   okadaic acid    CLO:0009575 run 9   proteomic profiling by mass spectrometry    1342_09.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_09.RAW   okadaic acid    0.1 uM
E1S10   Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   okadaic acid    CLO:0009575 run 10  proteomic profiling by mass spectrometry    1342_10.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_10.RAW   okadaic acid    0.1 uM
E1S11   Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   okadaic acid    CLO:0009575 run 11  proteomic profiling by mass spectrometry    1342_11.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_11.RAW   okadaic acid    0.1 uM
E1S12   Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   okadaic acid    CLO:0009575 run 12  proteomic profiling by mass spectrometry    1342_12.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/1342_12.RAW   okadaic acid    0.1 uM
E2S1    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 13  proteomic profiling by mass spectrometry    Elution_rest_a1.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a1.RAW   none    not applicable
E2S2    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 14  proteomic profiling by mass spectrometry    Elution_rest_a2.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a2.RAW   none    not applicable
E2S3    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 15  proteomic profiling by mass spectrometry    Elution_rest_a3.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a3.RAW   none    not applicable
E2S4    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 16  proteomic profiling by mass spectrometry    Elution_rest_a4.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a4.RAW   mercury dichloride  100 uM
E2S5    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 17  proteomic profiling by mass spectrometry    Elution_rest_a5.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a5.RAW   mercury dichloride  100 uM
E2S6    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 18  proteomic profiling by mass spectrometry    Elution_rest_a6.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a6.RAW   mercury dichloride  100 uM
E2S7    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   pervanadate CLO:0009575 run 19  proteomic profiling by mass spectrometry    Elution_rest_a7.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a7.RAW   pervanadate 25 uM
E2S8    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   pervanadate CLO:0009575 run 20  proteomic profiling by mass spectrometry    Elution_rest_a8.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a8.RAW   pervanadate 25 uM
E2S9    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   pervanadate CLO:0009575 run 21  proteomic profiling by mass spectrometry    Elution_rest_a9.RAW 1   1   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_a9.RAW   pervanadate 25 uM
E2S1    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 22  proteomic profiling by mass spectrometry    Elution_rest_b1.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b1.RAW   none    not applicable
E2S2    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 23  proteomic profiling by mass spectrometry    Elution_rest_b2.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b2.RAW   none    not applicable
E2S3    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   none    CLO:0009575 run 24  proteomic profiling by mass spectrometry    Elution_rest_b3.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b3.RAW   none    not applicable
E2S4    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 25  proteomic profiling by mass spectrometry    Elution_rest_b4.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b4.RAW   mercury dichloride  100 uM
E2S5    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 26  proteomic profiling by mass spectrometry    Elution_rest_b5.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b5.RAW   mercury dichloride  100 uM
E2S6    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   mercury dichloride  CLO:0009575 run 27  proteomic profiling by mass spectrometry    Elution_rest_b6.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b6.RAW   mercury dichloride  100 uM
E2S7    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   pervanadate CLO:0009575 run 28  proteomic profiling by mass spectrometry    Elution_rest_b7.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b7.RAW   pervanadate 25 uM
E2S8    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   pervanadate CLO:0009575 run 29  proteomic profiling by mass spectrometry    Elution_rest_b8.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b8.RAW   pervanadate 25 uM
E2S9    Mus musculus    immune system   B cell  not applicable  mercury poisoning   enrichment of phosphorylated protein    1   pervanadate CLO:0009575 run 30  proteomic profiling by mass spectrometry    Elution_rest_b9.RAW 1   2   AC=MS:1002038;NT=label free sample  NT=Trypsin;AC=MS:1001251    NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4    NT=Oxidation;MT=variable;TA=M;AC=UNIMOD:35  NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=variable NT=Phospho;MT=variable;TA=S,T,Y;AC=UNIMOD:21    NT=LTQ;AC=MS:1000447    https://ftp.ebi.ac.uk/pride-archive/2013/12/PXD000312/Elution_rest_b9.RAW   pervanadate 25 uM

Let me know if you'd like the file itself and I can send it over.

ypriverol commented 1 week ago

@kai-lawsonmcdowall if you want to review the PR let me know. https://github.com/bigbio/sdrf-pipelines/pull/169 You are more than welcome to the team.