Fengchao Yu   Fengchao Yu Ph.D, is a research faculty member of the Alexey Nesvizhskii group at the University of Michigan. Fengchao received his Ph.D. degree from the Hong Kong University of Science and Technology. He is currently the leading developer and maintainer of several proteomics data analysis tools including FragPipe, MSFragger, and IonQuant.

Integration of Skyline into FragPipe for Streamlined Visualization

Data visualization is an essential process in proteomics for assessing the quality of data and interpreting results. Skyline is a leader in this area, particularly for targeted and DIA methods. Here we present integration of Skyline with FragPipe, a comprehensive DDA and DIA proteomics data analysis pipeline, for visualizing and assessing FragPipe results. Read More
We have made it easy for FragPipe users to create Skyline documents and upload data to Skyline by bundling the "SkylineRunner" executable file in FragPipe, allowing users to create Skyline-compatible files with a single click. This new functionality supports both data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods. FragPipe automates the process by extracting and transferring all the required parameters from the FragPipe-generated workflow and manifest files to launch Skyline with the appropriate settings. For example, FragPipe passes to SkylineRunner filters that correspond to 1% protein and peptide false discovery rates (FDR) to ensure the high quality of identifications used to create the Skyline document file. For DDA, MSFragger in FragPipe produces pepXML files, with peptide-to-spectrum (PSM) matches subsequently rescored by MSBooster and Percolator or PeptideProphet. The pepXML files, spectra files, and the FDR-filtered protein file are utilized to create a Skyline document. In DIA workflows, FragPipe utilizes either DIA-Umpire to deconvolute DIA spectra before MSFragger search or MSFragger-DIA to search DIA spectra directly. The search results are then processed using MSBooster/Percolator, ProteinProphet, followed by EasyPQP for spectral library building and DIA-NN for quantification. The generated speclib and report.tsv files can be utilized as inputs to create a Skyline document. Alternatively, FragPipe can also create a Skyline document by utilizing pepXML files, spectra files, and FDR-filtered protein files as inputs, with the subsequent steps (spectral library building and quantification) performed by Skyline. We will demonstrate the benefits of FragPipe/Skyline integration using several representative DDA (LFQ-MBR workflow) and DIA datasets. Time permitting, we will also showcase the use of Skyline in the analysis of post-translational modification-enriched (e.g., glycoproteomics) data, and discuss opportunities and challenges for PTM analysis and visualization with Skyline.