Skyline v2.1 introduces fully integrated support for Bruker micrOTOF-Q and maXis series instruments.  The Skyline support for working with full-scan mass spectra has been extended to Bruker TOF instruments, and data acquired with them in several modes:

  • MS1 Filtering - chromatogram extraction from MS1 scans in data dependent acquisition (DDA) experiments
  • Targeted MS/MS (PRM) - chromatogram extraction from MS/MS scans in pseudo-SRM experiments
  • Data Independent Acquisition (DIA) - chromatogram extraction from MS/MS scans acquired in various isolation schemes
    • Consecutive wide windows
    • All Ions - alternating low energy and high energy scans of the entire instrument range

For more information on working with Skyline and Bruker TOF instruments, consult the following resources:

  • HUPO 2012 Bruker Lunch Seminar [PowerPoint][PDF]
  • Targeted Proteomics with Bruker TOF Instruments tutorial [PDF]

The following supporting files may also be useful:

  • Skyline template documents for Bruker TOF data analysis [ZIP]
  • Script for adding retention times to MGF files for peptide searches [Script]

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