Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF.

ABSTRACT: Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry-based proteomics because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation-serial fragmentation (dia-PASEF) on a Bruker trapped ion mobility (IM) separated quadrupole time-of-flight mass spectrometer. This requires alignment of the IM separation with the downstream mass selective quadrupole, leading to a more complex scheme for dia-PASEF window placement compared with DIA. To achieve high data completeness and deep proteome coverage, here we employ variable isolation windows that are placed optimally depending on precursor density in the m/z and IM plane. This is implemented in the freely available py_diAID (Python package for D

SUBMITTER: Skowronek P 

PROVIDER: S-EPMC9465115 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature