6533b82cfe1ef96bd128ec33

RESEARCH PRODUCT

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics.

Stefan TenzerUte DistlerJörg KuharevHansjörg SchildPedro NavarroYishai Levin

subject

IonsProteomicsReproducibilityProteomeSoftware toolCoverage dataCell BiologyBiologyProteomicsCollisionBioinformaticsMass spectrometryBiochemistryPeptide Fragmentsbody regionsTandem Mass SpectrometryProteomeHumansMolecular BiologyAlgorithmSoftwareBiotechnologyChromatography LiquidHeLa Cells

description

A data-independent acquisition (DIA) mass spectrometry approach, ultradefinition (UD)MSE, offers high reproducibility and improved proteome coverage over alternative DIA and data-dependent acquisition workflows. We present a data-independent acquisition mass spectrometry method, ultradefinition (UD) MSE. This approach utilizes ion mobility drift time-specific collision-energy profiles to enhance precursor fragmentation efficiency over current MSE and high-definition (HD) MSE data-independent acquisition techniques. UDMSE provided high reproducibility and substantially improved proteome coverage of the HeLa cell proteome compared to previous implementations of MSE, and it also outperformed a state-of-the-art data-dependent acquisition workflow. Additionally, we report a software tool, ISOQuant, for processing label-free quantitative UDMSE data.

yearjournalcountryeditionlanguage
2013-02-01Nature methods
10.1038/nmeth.2767https://pubmed.ncbi.nlm.nih.gov/24336358