Project description:Benchmarking Proteomics Quantitation in DIA-type data using real patient material to create a benchmark dataset comprising inter-patient heterogeneity

| EGAS00001005589 | EGA

ProteomicAnalysis(DIA)ofmuscleinvasivebladdercancerpatient-derivedxenografts

Project description:Accesstoproteomicfiles(DIA)ofMIBCpatient-derivedxenografts(N=8)

| EGAD00010002512 | EGA

4D-DIA proteomics and transcriptomics of thyroid cancer subtypes

Project description: Not available

| S-BSST1925 | biostudies-other

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.

Project description:Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we present a fast and sensitive approach for direct peptide identification from DIA data, MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based search engine MSFragger. Different from most existing methods, MSFragger-DIA conducts a database search of the DIA tandem mass (MS/MS) spectra prior to spectral feature detection and peak tracing across the LC dimension. To streamline the analysis of DIA data and enable easy reproducibility, we integrate MSFragger-DIA into the FragPipe computational platform for seamless support of peptide identification and spectral library building from DIA, data-dependent acquisition (DDA), or both data types combined. We compare MSFragger-DIA with other DIA tools, such as DIA-Umpire based workflow in FragPipe, Spectronaut, DIA-NN library-free, and MaxDIA. We demonstrate the fast, sensitive, and accurate performance of MSFragger-DIA across a variety of sample types and data acquisition schemes, including single-cell proteomics, phosphoproteomics, and large-scale tumor proteome profiling studies.

| S-EPMC10338508 | biostudies-literature

Proteomicanalysis(DIA)ofpatientswithnon-muscleinvasiveandmuscleinvasivebladdercancer

Project description:Accesstoproteomicfiles(DIA)ofpatientswithtreatment-naiveMIBC(N=51),treatment-naiveNMIBC(N=17)andneoadjuvantMIBC(N=11)

| EGAD00010002513 | EGA