title: Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device.
abstract: In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation-serial fragmentation (PASEF) enables hundreds of MS/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity.
authors.affiliation: Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Meier
authors.affiliation: Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Scarlet
authors.initials: S
authors.lastname: Beck
authors.affiliation: Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Niklas
authors.initials: N
authors.lastname: Grassl
authors.affiliation: Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Lubeck
authors.affiliation: Bruker Daltonics Inc., 40 Manning Road, Billerica, Massachusetts 01821, United States.
authors.forename: Melvin A
authors.initials: MA
authors.lastname: Park
authors.affiliation: Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Raether
authors.affiliation: Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
mesh_terms: D000595:Amino Acid Sequence; D004867:Equipment Design; D006367:HeLa Cells; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification; D020543:Proteome / Q000302:isolation & purification; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data; D053719:Tandem Mass Spectrometry / Q000295:instrumentation* / Q000379:methods* / Q000706:statistics & numerical data
chemical_list: D010446:Peptide Fragments; D020543:Proteome
keywords: MS/MS; TIMS; high resolution; ion mobility; multiplexing; peptide sequencing; proteomics; time-of-flight