Open AccessMaximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics
Author(s) -
Edna A. Trujillo,
Alexander S. Hebert,
Dain R. Brademan,
Joshua J. Coon
Publication year - 2019
Publication title -
analytical chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.117
H-Index - 332
eISSN - 1520-6882
pISSN - 0003-2700
DOI - 10.1021/acs.analchem.9b02979
Subject(s) - orbitrap , chemistry , mass spectrometry , shotgun proteomics , quadrupole ion trap , tandem mass spectrometry , hybrid mass spectrometer , ion trap , analytical chemistry (journal) , shotgun , top down proteomics , selected reaction monitoring , chromatography , proteomics , biochemistry , gene
Advances in tandem mass spectrometry (MS/MS) acquisition rate have steadily led to increased performance in shotgun proteomics experiments. To that end, contemporary mass spectrometers are outfitted with multiple analyzers allowing for the simultaneous collection of survey (MS1) and MS/MS spectra. In the latest generation Orbitrap hybrid, MS/MS scans can be acquired at a high rate using the dual cell linear ion trap analyzer, all while the next precursor is being dissociated in a collision cell and a MS1 scan is occurring in the Orbitrap. Often overlooked in these experiments is that the ion trap scan duration is highly variable and dependent upon precursor mass. Here, we examine the use of various static mass-to-charge ratio scan ranges for ion trap MS/MS acquisition and determine performance relative to conventional dynamic mass-to-charge ratio range scanning. We demonstrate that a fixed mass-to-charge ratio scan range can generate 12% more MS/MS scans and more unique peptide identifications as compared to the standard dynamic approach, respectively.