Diversity Matters: Optimal Collision Energies for Tandem Mass Spectrometric Analysis of a Large Set of N-Glycopeptides
Helga Hevér, Kinga Nagy, Andrea Xue, Simon Sugár, Kinga Komka, Károly Vékey, László Drahos, Ágnes Révész
Abstract
. Search engine dependence may also be noteworthy. Based on the trends, we designed an experimental method and tested it on HeLa, blood plasma, and monoclonal antibody samples. As compared to the literature, these notably lower collision energies in our workflow led to 10-50% more identified N-glycopeptides, with higher scores. We recommend a simple approach based on a small set of reference N-glycopeptides easily accessible from glycoprotein standards to ease the precise determination of optimal methods on other instruments. Data sets can be accessed via the MassIVE repository (MSV000089657 and MSV000090218).
Topics & Concepts
GlycopeptideWorkflowDatabase search engineCollisionFragmentation (computing)Search engineTandem mass spectrometryComputer scienceSet (abstract data type)Mass spectrometryChemistryDatabaseChromatographyInformation retrievalBiochemistryComputer securityAntibioticsOperating systemProgramming languageGlycosylation and Glycoproteins ResearchAdvanced Proteomics Techniques and ApplicationsRNA and protein synthesis mechanisms