Crux PSM search identifies very few PSM with q<=0.01

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Sangeetha R

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Sep 18, 2020, 5:34:13 AM9/18/20
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Dear Team,

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.  

.raw file converted to mzxml file using msconvert tool (CID, MS2, CST peak picking parameters

Crux 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_ind 

crux 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_ind 

Why I am getting very few PSMs with q value threshold of 0.01.
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