Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Bruker instruments

Bruker instruments for proteomics are currently divided into six families:

  • MALDI-TOF and TOF/TOF (e.g. rapifleX, ultrafleXtreme, autoflex maX)
  • timsTOF (e.g. timsTOF Ultra, timsTOF HT, timsTOF SCP)
  • QTOF (e.g. maXis II, impact II VIP QTOF)
  • Triple Quad
  • Ion Trap MS (amaZon speed ETD)
  • Magnetic Resonance Mass Spectrometry (solariX)

There are also several legacy models, such as Ultraflex, maXis, MALDI TOF microflex and micrOTOF.

Bruker instruments use five main data formats:

  • tdf format used by Bruker timsTOF instruments
  • baf format is used by Bruker QTOF instruments
  • yep format is used by both Bruker and Agilent Ion Traps
  • XMASS/XTOF/FID formats are typically used by Bruker MALDI instruments
  • tsf format used by Bruker MALDI-qTOF instruments for MALDI imaging and typically not proteomics experiments

Mascot DIA

We are working on adding diaPASEF support to Mascot DIA.

Mascot DDA

Mascot DDA is a spectrum-centric solution for DDA analysis. Mascot Server provides protein identification and Mascot Distiller raw data processing and quantitation. These processes can be automated using Mascot Daemon.

Mascot Distiller can process and visualise Bruker raw files in tdf, yep, baf, and XMASS/XTOF formats. Distiller processes them into high quality peak lists that can be saved or submitted direct to a Mascot Server for searching. The search results can be imported back into Distiller for further examination or used as the basis for quantitation.

Bruker tdf

Mascot Distiller has full support for tdf files containing DDA (Data-Dependent Acquisition) spectra. This includes ddaPASEF experiments. Ion mobility separation can be fully utilised, for example improving precursor quantitation results with ion mobility filtering.

Bruker yep

Mascot Distiller supports processing yep files containing PMF and DDA spectra.

Bruker baf

Mascot Distiller supports processing baf files containing PMF and DDA spectra.

Bruker XMASS/XTOF/FID

Mascot Distiller supports the XMASS/XTOF formats. Thes are actually folder structures and the data file is the FID file within the folder.

For most purposes, the XMASS/XTOF formats are no longer used in proteomics except in MALDI imaging experiments.

We recommend Mascot Daemon real time monitor. Configure it to process all the data files in a folder. Use “fast” as the file name or “1SRef”, depending on the exact files/version of Bruker software they were acquired with, not “*.fid”. The downside to this approach is that all the files are processed separately so you really need to run a second task to merge all the resulting mgf files into one and re-search.

MSConvert (DDA)

MSConvert is a component of ProteoWizard that converts between various file formats. It has a large number of options and can be configured as a data import filter in Mascot Daemon. Note that the input file format is not specified; msconvert auto-detects the format.