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]