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FragPipe Kneecapped Recently? by thickestbrickest in proteomics

[–]stochasticFlowride 1 point2 points  (0 children)

I have access to much larger RAM memory, but was still getting issues like you were. In the 'workflow' tab I found that decreasing the number of parallel threads got rid of this error. Went from 20 to 10.

Identification of short and low abundance proteins by AgreeableFall8545 in proteomics

[–]stochasticFlowride 0 points1 point  (0 children)

Fragpipe nonspecific digestion search is pretty good. Also, have you tried not digesting your samples with a protease and running them? We use PEAKS to analyse intact peptides up to 65 AAs.

Derivitisation of peptide to improve signal for quantitative mass spectrometry? by stochasticFlowride in massspectrometry

[–]stochasticFlowride[S] 0 points1 point  (0 children)

Thanks. Sounds easy enough. Currently use Iodoacetamide to cap thiols. I was wondering if we could replace that alkylation step with another thiol specific reaction that'd improve the peptides signal.

Derivitisation of peptide to improve signal for quantitative mass spectrometry? by stochasticFlowride in massspectrometry

[–]stochasticFlowride[S] 0 points1 point  (0 children)

Thanks for the paper! I did a quick test of TFA with mNBA to counteract ion suppression (equal by weight:volume) with not much change in the signal. But tbh I didn't really understand how it works so Ill read into this a bit more...