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diogobor / Scout

MS-cleavable search engine that enables interactomic analysis by identifying tandem mass spectra of cross-linked peptides.
MIT License
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multi-cv FAIMS runs #4

Closed grandrea closed 2 months ago

grandrea commented 3 months ago

hello,

I have crosslinking MS acquisitions performed with multiple control voltages on FAIMS device. Should i split the raw files by FAIMS CV? I am asking this because if Scout makes use of MS1retention time information then the chromatogram in the MS1 will be discontinuous as the instrument switches between voltages. How do you process such data?

many thanks!

diogobor commented 3 months ago

Hello,

Scout uses only the precursor m/z and precursor charge to identify the candidates. However, if you are interested to quantify the cross-linked peptides by using XIC, it would be better to split the RAW files.

Best, Diogo

grandrea commented 3 months ago

thanks!