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Nesvilab
Low resolution MS database search
Hi,
I'm interested in using the Labile search mode in MSFragger, but the tutorials mainly focus on high-resolution MS data. Could you please give some advice on setting validation and PTM module parameters for analyzing low-resolution MS data, specifically from OT-IT raw files? Thanks!
There is no big difference except for adjusting the fragment mass tolerance.
But I don't think low-resolution MS is good for the label search mode.
Best,
Fengchao
Thank you for clarifying this! I still have a few detailed questions:
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I'm still very interested in understanding why low-resolution MS isn't as suitable for Labile mode database search as high-resolution MS. Could you please provide some references or evidence to support this?
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Regarding the database search parameters for OT-IT data, do I only need to modify the "fragment mass tolerance" and "PTMProphet" parameters? I noticed that for ion trap MS with a resolution of 0.5 Da, the parameters seem to be set in PPM only. Could you please tell me how I should set these parameters?
Best wishes Baopu
Hi Baopu,
I'm still very interested in understanding why low-resolution MS isn't as suitable for Labile mode database search as high-resolution MS. Could you please provide some references or evidence to support this?
Because the fragment resolution is too low to have a good separation of different peaks and peptides. Labile mode normally has more fragment peaks to match. But maybe OK since it is a mass-offset search not an open search.
Regarding the database search parameters for OT-IT data, do I only need to modify the "fragment mass tolerance" and "PTMProphet" parameters? I noticed that for ion trap MS with a resolution of 0.5 Da, the parameters seem to be set in PPM only. Could you please tell me how I should set these parameters?
You can set in either Da or ppm unit. 0.5 Da or 300 ppm is fine as far as I know.
Best,
Fengchao