I am using Proteome Discoverer 2.3 to analyze TMT-labeled and phospho-enriched samples, but I am not getting any protein matches. I know there are relatively little peptides in these samples since the phospho-enriched sample is only 1-3% of the total proteins, so maybe there is a setting that I need to change to account for this?
I have the TMT label set as a static modification for the N-terminus and lysine residues, and oxidation (M) and phosphorylation (STY) as dynamic modifications. I have also set the strict FDR threshold to 0.03 instead of 0.01.
In the processing workflow I get the error:
"Spectrum Files RC: Warning: Couldn't calculate mass correction, because there are only 7 PSMs."
In the consensus workflow I get the error:
"Protein FDR Validator: Warning: Cannot validate proteins because all decoy proteins were filtered out"
Of note, I only used 8 of the 10 TMT labels in the 10-plex but have samples within this PD study that do use the other two, so for this particular sample I set the quan channels that weren't used to be controls rather than samples. But, I am wondering if the missing spectra from those two labels is causing the issue here.
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