Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant.

ABSTRACT: Ion mobility brings an additional dimension of separation to LC-MS, improving identification of peptides and proteins in complex mixtures. A recently introduced timsTOF mass spectrometer (Bruker) couples trapped ion mobility separation to TOF mass analysis. With the parallel accumulation serial fragmentation (PASEF) method, the timsTOF platform achieves promising results, yet analysis of the data generated on this platform represents a major bottleneck. Currently, MaxQuant and PEAKS are most used to analyze these data. However, because of the high complexity of timsTOF PASEF data, both require substantial time to perform even standard tryptic searches. Advanced searches (e.g. with many variable modifications, semi- or non-enzymatic searches, or open searches for post-translational m

SUBMITTER: Yu F 

PROVIDER: S-EPMC7996969 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature