title: The benefit of combining nLC-MALDI-Orbitrap MS data with nLC-MALDI-TOF/TOF data for proteomic analyses employing elastase.
abstract: The recently established coupling of a MALDI-type ion source to a linear ion trap and an orbitrap mass analyzer offers high-accuracy mass measurements compared to common MALDI-TOF/TOF instruments. Contrary to MALDI-TOF/TOF, the fragmentation of peptides in the new hybrid mass spectrometer is less efficient due to the generation of predominantly singly charged ions by the MALDI process. Therefore, data from two MALDI instruments, TOF/TOF and Orbitrap, were combined into a single data set in order to obtain accurate precursor masses as well as superior MS/MS spectra. This study demonstrates that an accurate precursor mass is particularly important for the nLC-MS/MS analyses of less-specific proteolytic digests. A potential gain of approximately one-third additional peptides identifications was theoretically estimated from previously published MALDI-TOF/TOF data. These calculations were verified by the nLC-MS/MS analysis of two elastatically digested proteomes, one cytosolic (Corynebacterium glutamicum) and one membrane (Halobacterium salinarium). Thereby it was discovered that the error distribution of a MALDI-Orbitrap can be significantly improved by applying an easy recalibration strategy. In summary, this study represents an updated workflow for the analysis of less-specific digests using nLC-MALDI.
authors.affiliation: Cluster of Excellence Macromolecular Complexes, Institute for Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Rietschel
authors.forename: Dominic
authors.initials: D
authors.lastname: Baeumlisberger
authors.forename: Tabiwang N
authors.initials: TN
authors.lastname: Arrey
authors.forename: Sandra
authors.initials: S
authors.lastname: Bornemann
authors.forename: Marion
authors.initials: M
authors.lastname: Rohmer
authors.forename: Malte
authors.initials: M
authors.lastname: Schuerken
authors.forename: Michael
authors.initials: M
authors.lastname: Karas
authors.forename: Bjoern
authors.initials: B
authors.lastname: Meyer
mesh_terms: D019843:Archaeal Proteins / Q000032:analysis / Q000235:genetics; D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods*; D048230:Corynebacterium glutamicum / Q000737:chemistry; D019617:Halobacterium salinarum / Q000737:chemistry; D010196:Pancreatic Elastase / Q000378:metabolism*; D010455:Peptides / Q000032:analysis* / Q000235:genetics; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000295:instrumentation / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D057188:Workflow
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D010455:Peptides; D010196:Pancreatic Elastase