What processing steps (for MSStatsTMT) are required for output from Trans Proteomics Pipeline?

[Debojyoti Pal]

Hello everyone

I am using Trans proteomics pipeline for TMT based analysis. Unfortunately, I have not come across any converter for the same. Please guide me on what processing steps are required. Here are the ones I could guess from other converters:

• Peptide ions which are shared by more than one protein to be removed
• If one spectrum has multiple identifications within one run, it only keeps the best identification with the minimal number of missing reporter ion intensities, highest reporter ion intensity, or lowest interference score if the information was available
• If a spectrum only has one or two reporter ion intensities within one MS run, it removes the spectrum from that run
• Ambiguous protein groups which contained multiple proteins were filtered out
• For fractionation, If a peptide ion was shared by multiple fractions, we kept the fraction with maximal average reporter ion abundance across all the channel in the fraction.

Do I need to ADD any other processing steps? Please let me know.

Regards

Debojyoti

PhD Student

[Debojyoti Pal]

Isnt "Peptide ions which are shared by more than one protein to be removed" and "Ambiguous protein groups which contained multiple proteins were filtered out" both essentially the same?

[Debojyoti Pal]

2) Further, what happens when the same peptide is identified by multiple spectra in the same run? How is that handled during processing?

3) And what does this mean "If one spectrum has multiple identifications within one run, it only keeps the best identification with the minimal number of missing reporter ion intensities, highest reporter ion intensity, or lowest interference score if the information was available" - are we talking about a single spectra giving multiple potential peptide matches???

[Mateusz Staniak]

Hi,

this list looks complete.

3) talks about multiple spectra per feature in a run (which answer 2).

All these operations required/assumed by MSstatsTMT are implemented in functions MSstatsConvert::MSstatsPreprocess and MSstatsConvert::MSstatsBalancedDesign. It's enough to put the data in MSstatsTMT 11(or so)-column format.

Kind regards,

Mateusz

[Debojyoti Pal]

Thank you Dr Mateusz. I was not aware of the tools that you mentioned. I think these would solve my problem.

Regards
Debojyoti