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ProteomicsImplementation of Non‑Isobaric TMT Analogues for Accurate Precursor‑Level Quantification by plexDIA
Multiplexed Data-Independent Acquisition (plexDIA) aims to bridge the gap between the quantitative depth of DIA and the sample throughput of isobaric tag-based workflows. Here, we implement non‑isobaric sample multiplexing using commercially available, isotopically differentiated tandem mass tag (TM...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2026-09-07 | PXD078770 | Pride
Plexdia Tko standard Non-isobaric multiplexing Quantitative proteomics 
UnknownIncreasing the throughput of sensitive proteomics by plexDIA.
Not available
S-EPMC9839897 | biostudies-literature
ProteomicsBenchmarking plexDIA analysis with SILAC-labelled Hela cell samples
SILAC labelled Hela cell lysates were mixed in defined ratios and analysed using both DDA and DIA methods, to serve as a benchmark for the novel plexDIA features of DIA-NN.
ORGANISM(S): Homo sapiens (Human) 
2023-10-19 | PXD039578 | Pride
Dia-nn Dia Hela Silac Plexdia 
ProteomicsApplying plexDIA analysis to newly synthesized proteome samples generated using a semi-automated enrichment protocol
Samples generated with a newly development semi-automated enrichment protocol for newly synthesized proteins, using different amounts of protein input, were analysed using data-independent acquisition (DIA) and processed with the plexDIA software features of DIA-NN (https://www.nature.com/articles/s...
ORGANISM(S): Homo sapiens (Human) 
2023-10-19 | PXD043817 | Pride
Silac Plexdia Quanpa 
ProteomicsBenchmarking of DDA and plexDIA analysis with SILAC-labelled Hela cell samples
SILAC labelled Hela cell lysates were mixed in defined ratios and analysed using both DDA and DIA methods, to serve as a benchmark for the novel plexDIA features of DIA-NN.
ORGANISM(S): Homo sapiens (Human) 
2023-10-19 | PXD039580 | Pride
Hela Silac Dda 
ProteomicsIncreasing the throughput of sensitive proteomics by plexDIA
Current mass-spectrometry methods enable high-throughput proteomics of large sample amounts, but proteomics of low sample amounts remains limited in depth and throughput. To increase the throughput of sensitive proteomics, we developed an experimental and computational framework, plexDIA, for simult...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2022-03-21 | MSV000089093 | MassIVE
ProteomicsCysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry
Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function, urging the need for accurate cysteine oxidation quantification to decode protein redox regulation. Here, we present a novel approach called CysQuant that enables simultaneous quantification...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-07-21 | PXD043895 | Pride
Cysteine oxidation Redox Data-independent acquisition Plexdia 
ProteomicsIncreasing the throughput of sensitive proteomics by plexDIA
Mass-spectrometry methods enable high-throughput proteomics with large input samples, but the depth and throughput of protein analysis remain limited for smaller samples. We aimed to increase throughput for analyzing limited samples while achieving high proteome coverage and quantitative accuracy. T...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) 
2021-11-02 | MSV000088302 | MassIVE
ProteomicsJMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics
Parallelization of data acquisition substantially increases the throughput of mass spectrometry-based proteomics. However, parallelization also increases the density of mass spectra and consequently the overlap between ions, frustrating their analysis. To improve sequence identification and quantifi...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2026-09-28 | PXD083370 | Pride
Astra Liver Mouse Plexdia Dia 
ProteomicsStrategies for increasing the depth and throughput of protein analysis by plexDIA
Raw files, spectral library, DIA-NN and Dinosaur outputs for "Strategies for increasing the depth and throughput of protein analysis by plexDIA"
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-11-04 | MSV000090650 | MassIVE
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