title: Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for chromatographic alignment and internal calibration.
abstract: Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.
authors.affiliation: Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands. n.m.palmblad@lumc.nl
authors.forename: Magnus
authors.initials: M
authors.lastname: Palmblad
authors.forename: Yuri E M
authors.initials: YE
authors.lastname: van der Burgt
authors.forename: Hans
authors.initials: H
authors.lastname: Dalebout
authors.forename: Rico J E
authors.initials: RJ
authors.lastname: Derks
authors.forename: Bart
authors.initials: B
authors.lastname: Schoenmaker
authors.forename: André M
authors.initials: AM
authors.lastname: Deelder
mesh_terms: D002138:Calibration; D005583:Fourier Analysis; D008970:Molecular Weight; D010455:Peptides / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D010455:Peptides