Proteome Discoverer with MSStatsPTM

[Scott Lyons]

Hello MSstats team,

I really appreciate all the work the group puts into making standardized proteomics analysis packages. Until recently I was making functions in R to analyze proteomics data but eventually ran into some issues when I had to normalize between multiple kits. Thats when I decided to jump ship to MSstats. A little background on my data, its TMT labeled, with a phosphoenriched fraction and an input fraction. All files were searched together in PD2.5.

The issue I'm having is trouble creating the ProteinName + PTM site annotation column. The PD PSMs PTM output file isn't great. It contains a column of modifications that contain all PTMs, if a site isn't perfectly localized it appeart to just choose 1. The other PTM column is ptmRS site column which contains all site and there localization probability. My question is how should i make the PTM annotation column?

I've read in previous posts here that you're still working on a function to convert the PD PTM output into an MSstats class file and wanted to know how that coming and if i could test  that out?

Appreciate the help.

Best,

Scott

[Devon Kohler]

Hi Scott,

So we do not currently have a converter for PD on the PTM side yet. I actually have not seen the exact output of PD PSMs PTM file. Would you be able to share a small snippet of your files? I'd be happy to put together a script you could use now to convert your data, and include it as dedicated converter in the next Bioconductor release.

Best,

Devon