Guo Ci Teo

May 30, 2024 | biorxiv.org | Kai Li |Guo Ci Teo |Kevin Yang |Fengchao Yu

AbstractData-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data.

Jul 27, 2023 | nature.com | Kevin Yang |Fengchao Yu |Guo Ci Teo |Markus Ralser

MSBooster workflowWorkflows with and without MSBooster are depicted in Fig. 1. In DDA experiments, MS/MS spectra are searched using MSFragger. For peptide identification from DIA data, either full MS/MS spectra are searched using MSFragger-DIA, or DIA-Umpire extracted pseudo-MS/MS spectra are searched using MSFragger as conventional DDA files. MSFragger produces pepXML and pin files, and the latter is used as input into MSBooster.