GlyComboCLI

GlyComboCLI is a command-line tool for the rapid assignment of monosaccharide combinations to observed and fragmented precursors in mass spectrometry experiments.

Given a list of observed precursor masses (from a plain text file or precursors selected for MS2 in an mzML file), GlyComboCLI performs a combinatorial search across user-defined monosaccharide building blocks and reports all compositions that fall within the specified mass error tolerance.

Key features

  • Accepts plain text mass lists (.txt) and vendor-neutral mzML files from Bruker, Thermo, Agilent, Waters, and Sciex instruments
  • Supports native, permethylated, and peracetylated derivatisations
  • Supports a wide range of reducing end labels including Free, Reduced, InstantPC, Rapifluor-MS, 2-AA, 2-AB, Procainamide, and Girard's reagent P, as well as custom reducing ends
  • Supports common adducts in both positive and negative ion mode
  • Outputs results as a CSV file, with an additional Skyline-compatible import file when mzML input is used
  • Supports up to five user-defined custom monosaccharides
  • Off-by-one isotope correction for cases of incorrect monoisotopic precursor selection

Quick example

GlyComboCLI.exe -F=".\masses.txt" -D=Native -R=Reduced -T=Da -E=0.6 -A=Neutral -hMax=9 -nMin=2 -nMax=10

Getting help