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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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ITRAQ/NeuCode and SILAC peptide quantification #255

Open trishorts opened 7 years ago

trishorts commented 7 years ago

I'm doing a check to see if we can id tmt-tagged peptides. Particularly interested in PTM-modified peptides as these haven't been quantifiable in the past. If I get good identification rate then we can talk about building in quant for reporter ions.

trishorts commented 7 years ago

This is working just fine now.

trishorts commented 7 years ago

Add ITRAQ/NeuCode and SILAC too

trishorts commented 7 years ago

TMT quantification should check each time for coisolation. Hopefully, the selected precursor will dominate MS1. If not, probable contamination. This is suspect quantification.

trishorts commented 7 years ago

TMT calibration should really focus calibrating reporter ions in MS2 to known reporter ions. Some are very close together.

rmillikin commented 7 years ago

TMT quantification currently works well in my fork for uncalibrated data. I have included some error-checking if the same diagnostic ion peak is used for close-mass plexes (ie the user picks too large of a tolerance to use for quantification).

Calibration is currently problematic for the diagnostic ions because small absolute changes in m/z from calibration result in large ppm changes. Even the error in ion-ion spacing can increase by ~10 fold. These ions should probably be treated differently by calibration since the charge state is known and the ppm can be used instead of the absolute m/z when calibrating

zrolfs commented 6 years ago

The issue with calibration would be fixed in #1315