OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Hannes Röst, Timo Sachsenberg, Stephan Aiche, +24

Nature Methods

EngineeringData ScienceMass SpectrometryMicro Total Analysis SystemData Integration +6

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Ben C. Collins, Christie L. Hunter, Yansheng Liu, +22

Nature Communications

A repository of assays to quantify 10,000 human proteins by SWATH-MS

George Rosenberger, Ching Chiek Koh, Tiannan Guo, +19

Scientific Data

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

Tiannan Guo, Petri Kouvonen, Ching Chiek Koh, +10

Nature Medicine

Proteomic TechnologyMedicineNatural SciencesBioanalysisMass Spectrometry +7

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

Vadim Demichev, Łukasz Szyrwiel, Fengchao Yu, +10

Nature Communications

A multicenter study benchmarks software tools for label-free proteome quantification

Pedro Navarro, Jörg Kuharev, Ludovic Gillet, +12

Nature Biotechnology

Functional GenomicsMedicineNatural SciencesComputational BiologyMolecular Biology +7

Building high-quality assay libraries for targeted analysis of SWATH MS data

Olga T. Schubert, Ludovic Gillet, Ben C. Collins, +8

Nature Protocols

Targeted AnalysisEngineeringBiomolecular ToolMedicineOmics Datasets +11

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

Ben C. Collins, Ludovic Gillet, George Rosenberger, +4

Nature Methods

14-3-3 SystemBiochemistryInteractomicsMedicineNatural Sciences +11

Quantitative proteomics: challenges and opportunities in basic and applied research

Olga T. Schubert, Hannes Röst, Ben C. Collins, +2

Nature Protocols

Proteomic TechnologyBiochemistryMedicineNatural SciencesBioanalysis +9

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

George Rosenberger, Isabell Bludau, Uwe Schmitt, +13

Nature Methods

EngineeringStatistical ControlMedicinePeptide LibraryProtein Error Rates +10