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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Does MSGF+ support Bruker TDF files? #155

Open hxxhust163 opened 1 month ago

hxxhust163 commented 1 month ago

Hi MSGF+ Team

Thanks for your work in MSGF+.

I get mass spectrometry data from Bruker TimsTOF and want to do database search using MSGF+.

*At first, I convert the .d files into mzML. But for the 'Fragmentation Method' and 'Instrument ID', how should I set? I tried both 3 as follows but got an error showing 'mzML does not have any valid spectra'. Can you please help figure this out? Thanks very much!

Fragmentation Method 0 means as written in the spectrum or CID if no info (Default) 1 means CID 2 means ETD 3 means HCD 4 means UVPD FragmentationMethodID=3

Instrument ID 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra, or with only low-res HCD spectra 1 means High-res LTQ (Default for high res HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos instruments with high res MS2 spectra 2 means TOF 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments InstrumentID=3

**

Best wishes Xiaoxiang

alchemistmatt commented 1 month ago

MS-GF+ is designed for spectra where a parent ion has been isolated with a narrow m/z window, then is fragmented by CID, ETD, or HCD, yielding a fragmentation pattern of a single peptide. It is not compatible with timsTOF fragmentation spectra. You will either need to use commercial software designed for timsTOF PASEF spectra, or use MSFragger.

hxxhust163 commented 1 month ago

OK. Thanks!