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ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2016-09-27 | PXD002952 | Pride
Lfqbench Lfq Swath-ms Benchmark 
ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2017-04-27 | MSV000081024 | MassIVE
UnknownA multicenter study benchmarks software tools for label-free proteome quantification.
Not available
S-EPMC5120688 | biostudies-literature
ProteomicsApply LFQBench and evaluate with FASP and ISD
In this study, we developed an automated high-throughput proteomics sample preparation workflow (AutoDEP) with a commercially available 96-well DNA extraction plate on the Biomek i7 liquid handling system tailored for industrial microorganisms.
ORGANISM(S): Corynebacterium Glutamicum Atcc 13032 
2025-12-23 | PXD072341 |
ProteomicsUnifying the analysis of bottom-up proteomics data with CHIMERYS
Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography–tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) Mus musculus (Mouse) Halobacterium salinarum Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2025-04-16 | PXD053241 | Pride
Dia Human Fdr Chimerys Entrapment Multi-species Lc-msms Dda 
ProteomicsHigh-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA
The ability to conduct high-quality proteomic experiments in high throughput has opened new avenues in clinical research, drug discovery, and systems biology. Next to an increase in quantitative precision, recent developments in high-throughput proteomics have also gained proteomic depth, to the ext...
ORGANISM(S): Cicer arietinum (Chickpea) (Garbanzo) Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2022-12-01 | PXD036786 | Pride
Dia Zeno swath 
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