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MetabolomicsCombining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Spring wheat (Triticum aestivum L.) was grown in a free-air carbon dioxide (CO2) enrichment (FACE) field experiment. Grain and biomass yield and its components were determined at maturity and the grain metabolome was analysed by gas chromatography-mass spectrometry (GC-MS) for elevated and ambient C...
2012-09-21 | MTBLS21 | MetaboLights
ProteomicsHuman Breast Milk TMT labeled Rescored with Prosit
We Have human breast milk dataset in this project. We predict all spectra in the datasets via Prosit then rescore. We have 100% FDR maxquant search results, and using percolator we get 1%FDR filtered results with andromeda Scores and another with features extracted from Prosit predictions.
ORGANISM(S): Homo sapiens (Human) 
2022-05-26 | PXD030339 | Pride
Human Ms3 Tmt11plex Breast milk It Iontrap 
ProteomicsProsit-XL: enhanced cross-linked peptide identification by accurate fragment intensity prediction to study protein-protein interactions and protein structures
It has been shown that integrating peptide property predictions such as fragment intensity into the scoring process of peptide spectrum match can greatly increase the number of confidently identified peptides compared to using traditional scoring methods. Here, we introduce Prosit-XL, a robust and a...
ORGANISM(S): Homo sapiens (Human) Cytomegalovirus 
2025-05-18 | PXD057705 | Pride
Deep learning Crosslinking mass spectrometry 
ProteomicsHuman Yeast Dilution TMT labelled Rescored with Prosit.
We Have a human yeast dilution dataset in this project. We predict all spectra in the datasets via Prosit then rescore. We have 100% FDR max quant search results using percolator. In addition, we get 1%FDR filtered results with andromeda Scores and another with features extracted from Prosit predict...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2022-06-09 | PXD030340 | Pride
Human Cid Ot Yeast Hcd Tmt11plex It Orbitrap Iontrap 
ProteomicsPancreatic cell lines MS2/MS3 TMT labeled Rescored with Prosit
We Have a pancreas MS2/MS3 dataset in this project. We predict all spectra in the datasets via Prosit then rescore. We have 100% FDR maxquant search results, and using percolator we get 1%FDR filtered results with andromeda Scores and another with features extracted from Prosit predictions.
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD030342 | Pride
Human Ms3 Ms2 Ot Tmt11plex It Orbitrap Iontrap 
OtherMass-spectrometry-based draft of the human proteome
Data from ProteomeXchange, PXD ID: PXD000865. File: 00645_A01_P004893_B0A_A00_R1.mzml. Published as part of Nature 509, 582-587, 29 May 2014.
ORGANISM(S): Homo_sapiens_viruses, Human 
GPM32310000771 | GPMDB
Resource Reanalysis 
Proteomics,MultiomicsA deep proteome and transcriptome abundance atlas of 29 healthy human tissues
We generated a systematic, quantitative and deep proteome and transcriptome abundance atlas from 29 paired healthy human to serve as a molecular baseline to study human biology.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-03-02 | MSV000083508 | MassIVE
ProteomicsA proteomic atlas of the common wheat
Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we built the first global quantitative atlas containing transcriptomes, proteomes, phospho-proteomes and acetyl-proteomes of 20 tissues in common whea...
ORGANISM(S): Triticum Aestivum 
PXD041703 |
ProteomicsPharmacoproteomic characterisation of human colon and rectal cancer - CRC65 Full Proteomes
Most molecular cancer therapies act on protein targets but data on the proteome status of patients and cellular models are only beginning to emerge. Here, we profiled the proteomes of 65 colorectal cancer (CRC) cell lines to a depth of >10,000 proteins using mass spectrometry. Integration with prote...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-11-23 | MSV000081738 | MassIVE
ProteomicsProteomic diversity in bacteria: Insights and implications for bacterial identification
We acquired the largest bacterial proteomic resource, covering 303 species, 119 genera, and five phyla. The proteome coverage is, on average, over 50%. Additionally, we acquired further datasets for bacterial identification algorithm validation: i) 303 species at a 30-minute gradient (38 samples per...
ORGANISM(S): Bacteria (ncbitaxon:2) 
2024-12-06 | MSV000096603 | MassIVE
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