Comments (2)
Hi Dave,
thanks for the insights! Makes totally sense how you describe it :)
I'll test out the QValue and PepQValue as quality control filters and see which one works better!
Thanks again!
Best,
Konrad
from informed-proteomics.
Hi, Konrad.
Because I routinely run MSPathFinderT with only target sequences, I filter PrSMs to require e-values below 0.01 (a similar rule exists in TopPIC) and Probability scores above 0.5. It sounds as though you are running your searches on both target and decoy sequences, so you are in better shape for hitting a particular TDA-estimated FDR. Yes, you can probably just retain the QValues below some maximum to achieve that FDR. I believe PepQValue will be differentiated from QValue by the fact that some proteoforms match multiple spectra; if you're computing FDR by estimated erroneous proteoforms rather than PrSMs, you could go that route instead.
Good luck!
Dave
from informed-proteomics.
Related Issues (20)
- How to install? HOT 2
- Error computing FDR: Cannot compute FDR Scores; target file is empty HOT 1
- Why am I running MSPathFinder slow? HOT 4
- What does this warning mean? HOT 5
- Why does the identified PrSM decrease a lot after using the modified file? HOT 1
- Why is there no data in the generated 2DLC_H3_1.ms1ft file?
- Can ProMex be used to extract feature from bottom up data HOT 1
- Why is there no data in the generated RP4H_P32_WHIM2_biorep1_techrep3.ms1ft when RP4H_P32_WHIM2_biorep1_techrep3.ms1ft runs ProMex?
- Reported proteoform masses is always 9Da less HOT 2
- Is there any way to batch export XIC data points(time & Intensity) of all PrSMs? HOT 2
- ProMex feature determination: Mass HOT 2
- Is MSPathFinderT able to report isobaric proteoforms? HOT 3
- Issues in searching Thermo EThcD raw data
- limiting search by mass, charge and seqence length HOT 1
- Promex csv error
- Output deconvoluted spectra for external visualization/analysis
- General help
- Analysis of profile data MSPathFinder HOT 4
- Sequence contains no elements HOT 1
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from informed-proteomics.