Fengchao Yu

1 month ago | nature.com | Fengchao Yu |Yamei Deng |Alexey I. Nesvizhskii

Liquid chromatography-mass spectrometry based proteomics, particularly in the bottom-up approach, relies on the digestion of proteins into peptides for subsequent separation and analysis. The most prevalent method for identifying peptides from data-dependent acquisition mass spectrometry data is database search. Traditional tools typically focus on identifying a single peptide per tandem mass spectrum, often neglecting the frequent occurrence of peptide co-fragmentations leading to chimeric spectra. Here, we introduce MSFragger-DDA+, a database search algorithm that enhances peptide identification by detecting co-fragmented peptides with high sensitivity and speed. Utilizing MSFragger’s fragment ion indexing algorithm, MSFragger-DDA+ performs a comprehensive search within the full isolation window for each tandem mass spectrum, followed by robust feature detection, filtering, and rescoring procedures to refine search results. Evaluation against established tools across diverse datasets demonstrated that, integrated within the FragPipe computational platform, MSFragger-DDA+ significantly increases identification sensitivity while maintaining stringent false discovery rate control. It is also uniquely suited for wide-window acquisition data. MSFragger-DDA+ provides an efficient and accurate solution for peptide identification, enhancing the detection of low-abundance co-fragmented peptides. Coupled with the FragPipe platform, MSFragger-DDA+ enables more comprehensive and accurate analysis of proteomics data. Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation window, improving sensitivity and maintaining strict false discovery rate control.

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.