Multiplexed peptide analysis using data-independent acquisition and Skyline.

ABSTRACT: Here we describe the use of data-independent acquisition (DIA) on a Q-Exactive mass spectrometer for the detection and quantification of peptides in complex mixtures using the Skyline Targeted Proteomics Environment (freely available online at http://skyline.maccosslab.org). The systematic acquisition of mass spectrometry (MS) or tandem MS (MS/MS) spectra by DIA is in contrast to DDA, in which the acquired MS/MS spectra are only suitable for the identification of a stochastically sampled set of peptides. Similarly to selected reaction monitoring (SRM), peptides can be quantified from DIA data using targeted chromatogram extraction. Unlike SRM, data acquisition is not constrained to a predetermined set of target peptides. In this protocol, a spectral library is generated using data-dependen

SUBMITTER: Egertson JD 

PROVIDER: S-EPMC5127711 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature