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ProteomicsBenchmarking CHIMERYS using Wide Window Acquisition and Classical Narrow Isolation Window Data Dependent Acquisition
A comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yield-ed impressive results, current studies suffer from a limited proteomic depth and dynamic range there-for...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2024-02-13 | PXD045500 | Pride
E. coli Wide window acquisition Yeast Direct injection Micropillar array chromatography Vanquish neo Hela Orbitrap exploris 480 Single cells Trap-and-elute 
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 
ProteomicsWide Window Acquisition and AI-based data analysis to reach deep proteome coverage for a wide sample range, including single cell proteomic inputs – Co-immunoprecipitation samples
A comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yielded impressive results, current studies suffer from a limited proteomic depth and dynamic range therefore ...
ORGANISM(S): Mus musculus (Mouse) 
2024-02-13 | PXD037985 | Pride
Mus musculus Co-immunoprecipitation Micropillar array chromatography Smarca5 Orbitrap exploris 480 Ultimate3000 rslcnano Protein-protein interactions Trap-and-elute 
ProteomicsLive Electrophoresis-Correlative AI Democratizes Single-cell Mass Spectrometry Proteomics
The goal of this project was to deepen proteome coverage on broadly accessible mass spectrometers. We developed electrophoresis-correlative (Eco) ion sorting mass spectrometry (MS) on a decade-old quadrupole orbitrap mass spectrometer (Q Exactive Plus, Thermo). Artificial intelligence (AI) was adapt...
ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog) 
2025-08-16 | PXD062702 | Pride
Single-cell proteomics Mass spectrometry Artificial intelligence Capillary electrophoresis 
UnknownReal-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.
Not available
S-EPMC12582007 | biostudies-literature
ProteomicsImpact of variations in standard operating procedure on plasma proteome recovery
Advancements in mass spectrometry and complementary technologies now enable comprehensive and high-resolution plasma proteomics. Plasma is a key biofluid for clinical research, harboring potential disease informative biomarkers. Commercial sources of non-diseased, healthy donor plasma samples are of...
ORGANISM(S): Homo sapiens (Human) 
2026-04-13 | PXD069325 | Pride
Mass spectrometry Clinical proteomics Biofluids Data-independent acquisition 
ProteomicsImpact of variations in standard operating procedure on plasma proteome recovery
Advancements in mass spectrometry and complementary technologies now enable comprehensive and high-resolution plasma proteomics. Plasma is a key biofluid for clinical research, harboring potential disease informative biomarkers. Commercial sources of non-diseased, healthy donor plasma samples are of...
ORGANISM(S): Homo sapiens (Human) 
2026-04-13 | PXD069212 | Pride
Mass spectrometry Clinical proteomics Biofluids Data-independent acquisition 
Proteomics15 cm Aurora Gen3 column benchmarking on an Exploris 480
A comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yield-ed impressive results, current studies suffer from a limited proteomic depth and dynamic range there-for...
ORGANISM(S): Homo sapiens (Human) 
2024-02-13 | PXD045457 | Pride
Vanquish neo Orbitrap exploris 480 Trap-and-elute 
ProteomicsWide-Window Acquisition Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics
The sensitivity of single-cell proteomics (SCP) has increased dramatically in recent years due to advances in experimental design, sample preparation, separations and mass spectrometry instrumentation. However, further increasing the sensitivity of SCP methods and instrumentation will enable the stu...
ORGANISM(S): Homo sapiens (Human) 
2023-07-11 | PXD037527 | Pride
Label-free Proteome Single-cell proteomics Wide-window acquisition 
ProteomicsBenchmarking of 5.5 cm, 50 cm and 110 cm micropillar array columns as compared to packed bed columns
A comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yield-ed impressive results, current studies suffer from a limited proteomic depth and dynamic range there-for...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2024-02-13 | PXD039576 | Pride
E. coli Yeast Direct injection Micropillar array chromatography Vanquish neo Hela Orbitrap exploris 480 Trap-and-elute 
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