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Vitek-Lab / MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments
https://vitek-lab.github.io/MSstatsPTM/
Artistic License 2.0
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Converter for PaSER (DIA) matrix to MSstatsPTM ? #65

Open JieXue22 opened 1 year ago

JieXue22 commented 1 year ago

Dear MSstatsPTM developers,

I have a peptides matrix generated from PaSER. It's a tsv. file and the PTMs are represented with UniMod Accession #. Could you please add a converter for this platform?? The header format is below:

Protein.Group Protein.Ids Protein.Names Genes First.Protein.Description Proteotypic Stripped.Sequence Modified.Sequence Precursor.Charge Precursor.Id sample 1 sample 2 sample 3 sample 4 sample 5 sample 6 sample 7 sample 8 sample 9 sample 10
P55011 P55011 S12A2_HUMAN SLC12A2 Solute carrier family 12 member 2 1 AAAAAAAAAAAAAAAGAGAGAK AAAAAAAAAAAAAAAGAGAGAK 2 AAAAAAAAAAAAAAAGAGAGAK2 intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity

Thank you!

devonjkohler commented 11 months ago

Hi @JieXue22,

I have never seen the output of PaSER. Could you shoot me over some data for this? I can look into the converter if I have the data.

Devon