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Nesvilab / PTM-Shepherd

A tool for summarizing open search results
http://ptmshepherd.nesvilab.org
Apache License 2.0
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FragPipe results #14

Closed MartinaBartolucci closed 3 years ago

MartinaBartolucci commented 3 years ago

Hello,

in the global.profile file released by Offset search for PTMs with FragPipe I can't understand the meaning of the column [experiment] _percent_also_in_unmodified, can you clarify what the reported data means? Thanks for the attention. Martina

sarah-haynes commented 3 years ago

Hi Martina, we have descriptions of FragPipe output files here, see global.profile.tsv here.

Sarah

MartinaBartolucci commented 3 years ago

Thanks, unfortunately I have already read those and I do not understand the percentage to what it refers. Can I use this parameter as a comparison between mutated and not?

danielgeiszler commented 3 years ago

Hi Martina,

Can you elaborate on what it is you're doing? The mass offset search is not designed to look for mutations, it's designed to look for PTMs.

This column is simply the percentage of PSMs with that PTM that has a corresponding unmodified PSM.

MartinaBartolucci commented 3 years ago

Sorry, modified, not mutated. I have 4 groups of samples and I need to see if there are any proteins with modifications due to the A to I editing of the RNA. I calculated all the mass differences of the possible amino acid substitutions and used them for the offset search. Now among the results of the offset search I would like to understand which is the best parameter that allows me to compare the different groups of samples. Thanks again.

danielgeiszler commented 3 years ago

The [experiment] _percent_also_in_unmodified column is telling you how many modified PSMs within that group have a matched unmodified PSM.

If you're looking to compare the number of mutations between groups, then you'd probably just want to use the PSM counts or the [experiment]_percent PSMs themselves.