Does MSGF+ support Bruker TDF files?

[hxxhust163]

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]

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]

OK. Thanks!