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ProteomicsiTRAq and TMTPro datasets Rescored with Prosit
Rescoring with Prosit predictions and percolator 6 different PRIDE submited datasets: 1- PXD017472 2- PXD017621 3- PXD002214 4- PXD021401 5- PXD027089 6- PXD024275
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2022-06-09 | PXD031575 | Pride
Human Tmtpro Prosit Itraq4 Mouse Itraq8 Tmt16plex Tmt18plex 
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 
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 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 
UnknownProsit Transformer: A transformer for Prediction of MS2 Spectrum Intensities.
Not available
S-EPMC9087333 | biostudies-literature
UnknownProsit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.
Not available
S-EPMC12214610 | biostudies-literature
UnknowninSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction.
Not available
S-EPMC9720494 | biostudies-literature
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 
ProteomicsProsit: Proteome-wide prediction of peptide tandem mass spectra by deep learning
In this study, we extended the ProteomeTools peptide library (PROPEL, see PXD004732 and PXD010595) to train a deep neural network resulting in chromatographic retention time and fragment ion intensity predictions for (tryptic) peptides that exceed the quality of the experimental data.
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Caenorhabditis Elegans (ncbitaxon:6239) 
2021-03-12 | MSV000087047 | MassIVE
ProteomicsDeep learning boosts immunopeptidomics one mass spectrum at a time
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune oncology. Still, the identification of such non-tryptic peptides presents substantial computational challenges. To address these, we synthesized...
ORGANISM(S): Homo sapiens (Human) 
2021-04-26 | PXD021398 | Pride
Hla peptide Rescoring Fragmentation prediction Spectra prediction Ligand Hla class i Proteometools Spliced peptide Proteasomal splicing Deep learning Prosit 
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