Dear Professors,I am a beginner in using the crux software. I have tried running the tide- search to extract all peptide spectrum matches. From the resulting xcorr score, when I calculate the number of PSM with a q-value threshold of 0.01, I am getting very few PSMs around 10. I doubted whether I have some mistakes in querying.the raw file used: Orbitrap XL CID-IT Yeast from https://chorusproject.org/pages/dashboard.html#/projects/all/819/experiments/1430/files.raw file converted to mzxml file using msconvert tool (CID, MS2, CST peak picking parametersCrux commands used:crux tide-index --decoy-format shuffle --enzyme trypsin --max-length 21 --clip-nterm-methionine T --mods-spec C+57.02146 yeast.fasta yeast_indcrux tide-search --max-precursor-charge 3 --pepxml-output T --file-column T --top-match 1 --concat T --precursor-window 1 --precursor-window-type mass --remove-precursor-peak T B01a_130417_Yeast_long.mzXML yeast_indWhy I am getting very few PSM with q value threshold of 0.01.--
You received this message because you are subscribed to the Google Groups "crux-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to crux-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/crux-users/44056b5e-e88c-47a3-b94e-a5d4d0a5b4dan%40googlegroups.com.
I have separately calculated the q-value for each PSM using xcorr score and target/decoy assignment in search result.
To view this discussion on the web visit https://groups.google.com/d/msgid/crux-users/47ab3a49-f9d1-4084-a8e5-a8e31cb27538n%40googlegroups.com.
--mz-bin-width <float>– Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default =
To view this discussion on the web visit https://groups.google.com/d/msgid/crux-users/7a62c4e3-752c-44f1-93b0-6cad1f69daf1n%40googlegroups.com.