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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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FragPipetoMSstatsPTMFormat - LFQ #74

Closed kaupuks closed 7 months ago

kaupuks commented 9 months ago

Hello,

What files should be submitted to import LFQ data (Phospho) from fragpipe?

msstats_data = FragPipetoMSstatsPTMFormat("MSstats.csv", "experiment_annotation.tsv", mod_id_col = "STY", localization_cutoff=.75, label_type="LF", remove_unlocalized_peptides=TRUE)

FASTA file not provided and Start column missing from data. MSstatsPTMSiteLocator requires one of these to be provided to identify modification site number

Best Regards, Algirdas

devonjkohler commented 9 months ago

Hi Algirdas,

I think your problem is that you are passing strings to the function and not the loaded data.frames. Try to load this data into R and pass that object to the function.

One note, FragPipe should automatically add your annotation information directly into the msstats.csv file so you should not need to use an annotation file.

Example code below.

Best, Devon

input_data = read.csv("msstats.csv")
annotation = read.csv("experiment_annotation.tsv", sep="\t")

msstats_data = FragPipetoMSstatsPTMFormat(input_data,
annotation,
mod_id_col = "STY",
localization_cutoff=.75, label_type="LF",
remove_unlocalized_peptides=TRUE)
kaupuks commented 9 months ago

Hello,

Thanks for answer, but error is the same. Is it ok with mstats.csv ?

head(input_data) ProteinName PeptideSequence PrecursorCharge FragmentIon 1 sp|A0A1B0GTU1|ZC11B_HUMAN RLS[79.9663]SAST[79.9663]GKPPLSVEDDFEK 3 NA 2 sp|A0A1B0GTU1|ZC11B_HUMAN RLS[79.9663]SAST[79.9663]GKPPLSVEDDFEK 3 NA 3 sp|A0A1B0GTU1|ZC11B_HUMAN RLS[79.9663]SAST[79.9663]GKPPLSVEDDFEK 3 NA 4 sp|A0A1B0GTU1|ZC11B_HUMAN RLS[79.9663]SAST[79.9663]GKPPLSVEDDFEK 3 NA 5 sp|A0A1B0GTU1|ZC11B_HUMAN RLS[79.9663]SAST[79.9663]GKPPLSVEDDFEK 3 NA 6 sp|A0A1B0GTU1|ZC11B_HUMAN RLS[79.9663]SAST[79.9663]GKPPLSVEDDFEK 3 NA ProductCharge IsotopeLabelType Condition BioReplicate Run Intensity 1 NA L pancr 1 P175_1 NA 2 NA L pancr 1 P175_2 NA 3 NA L pancr 2 P280_1 732186.1 4 NA L pancr 2 P280_2 NA 5 NA L pancr 3 P286_1 NA 6 NA L pancr 3 P286_2 NA

Best, Algirdas

devonjkohler commented 9 months ago

Hi Algirdas,

Apologies I should foreseen this problem. FragPipe just added PTM info to the label free msstats output a month or so ago and it has not made it into the release version yet (see https://github.com/Vitek-Lab/MSstatsPTM/issues/73 for the same discussion). You will need to check with the developers of FragPipe for the correct version, you may have to download the development version of the platform for this but I am not positive.

This will be resolved in the next release of FragPipe going forward.

kaupuks commented 9 months ago

It's clear now, thanks!