Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP.

ABSTRACT: Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20 m/z), and gradient time (60 min).

SUBMITTER: Wang J 

PROVIDER: S-EPMC12379512 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature