title: SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS data.
abstract: We present a software algorithm that combines ion trap and orbitrap product ion spectra acquired in parallel. The hybrid product ion spectra identify more peptides than when using two separate searches for the orbitrap and LTQ data. The program extracts the high-accuracy mass data from the Orbitrap mass analyzer and combines it with the high-sensitivity data analyzed in the LTQ linear ion trap; the m/z values of the high-confidence fragment ions are corrected to orbitrap mass accuracies and the fragment ion intensities are amplified. This approach utilizes the parallel spectrum measurement capabilities of the LTQ-Orbitrap. We present our approach to handling this type of hybrid data, explain our alignment program, and discuss the advantages of the chosen methodology.
authors.affiliation: Department of Pathology, Harvard Medical School and Children's Hospital Boston, Boston, MA 02115, USA. flavio.monigatti@childrens.harvard.edu
authors.forename: Flavio
authors.initials: F
authors.lastname: Monigatti
authors.forename: Hanno
authors.initials: H
authors.lastname: Steen
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods; D008969:Molecular Sequence Data; D012984:Software; D013223:Statistics as Topic / Q000379:methods*; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000032:analysis*
chemical_list: D029961:Zebrafish Proteins