RT Journal Article
SR Electronic
T1 Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 656207
DO 10.1101/656207
A1 Florian Meier
A1 Andreas-David Brunner
A1 Max Frank
A1 Annie Ha
A1 Eugenia Voytik
A1 Stephanie Kaspar-Schoenefeld
A1 Markus Lubeck
A1 Oliver Raether
A1 Ruedi Aebersold
A1 Ben C. Collins
A1 Hannes L. Röst
A1 Matthias Mann
YR 2019
UL http://biorxiv.org/content/early/2019/05/31/656207.abstract
AB Bottom-up proteomics produces complex peptide populations that are identified and quantified at the precursor or fragment ion level. Data dependent acquisition methods sequentially isolate and fragment particular precursors, whereas data independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling deterministically through segments of a predefined precursor m/z range. Although the selection windows of DIA collectively cover the entire mass range of interest, only a few percent of the ion current are sampled due to the consecutive selection of acquisition windows. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current. We analyze the acquired data by extending established targeted data extraction workflow for the analysis of DIA data by the additional ion mobility dimension, providing additional specificity in the precursor identification. Data acquired from simple protein mixtures verify the expected data completeness and data in single runs of a whole proteome digest demonstrate deep proteome coverage and a very high degree of reproducibility and quantitative accuracy, even from 10 ng sample amounts.