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ProteomicsTetranychus urticae secretome - The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae: A Quest for Effectors
The two-spotted spider mite Tetranychus urticae is an extreme polyphaguous crop pest. Next to an increased detoxification potential of plant secondary metabolites, it has recently been shown that spider mites manipulate plant defences. Salivary constituents are proposed to play an important role dur...
ORGANISM(S): Tetranychus urticae (Two-spotted spider mite) 
2017-01-17 | PXD003022 | Pride
Tetranichus urticae Secretome 
ProteomicsmESC shotgun and positional proteomics based on deep proteome sequence database (derived from RIBOseq data)
Shotgun and positional proteomics study of a mouse embryonic stem cell line. We devised a proteogenomic approach constructing a custom protein sequence search space, built from both SwissProt and RIBO-seq derived translation products, applicable for LC-MSMS spectrum identification. To record the im...
ORGANISM(S): Mus musculus (Mouse) 
2013-02-25 | PXD000124 | Pride
Ribo-seq Shotgun Ribosome profiling Swissprot Mesc 14 N-terminal cofradic 
ProteomicsSpectral prediction features as a solution for the search space size problem in proteogenomics
Proteogenomics approaches often struggle with the distinction between right and false peptide-to-spectrum matches as the database size enlarges. However, features extracted from tandem mass spectrometry intensity predictors can enhance the peptide identification rate and can provide extra confidence...
ORGANISM(S): Homo sapiens (Human) 
2021-03-26 | PXD022280 | Pride
Proteogenomics  spectrum predictor  nanopore sequencing  ribosome profiling  rna-seq  ms2pip  prosit  intensity features  machine learning  hct116  percolator  maxquant 
ProteomicsPROTEOFORMER 2.0: MS validation
PROTEOFORMER is a pipeline for generating a search space of candidate translation products based on ribosome profiling data. The pipeline was published in 2014, but since then, several features have been added. For this project, the PROTEOFORMER pipeline 2.0 was tested on human HCT116 and Jurkat cel...
ORGANISM(S): Homo sapiens (Human) 
2019-05-03 | PXD011353 | Pride
Jurkat Proteoformer Hct116 Msms 
ProteomicsM.musculus - Whole organism, Empai (Menschaert,mcp,2013)
abundance based on MAPPED_BY_AUTHORS, emPAI, Interaction consistency score: 3.6, Coverage: 13
ORGANISM(S): 10090 
2013-00-00 | 61138479 | PAXDB
ProteomicsM.musculus - Whole organism, Nsaf (Menschaert,mcp,2013)
abundance based on MAPPED_BY_AUTHORS, NSAF, Interaction consistency score: 5.2, Coverage: 13
ORGANISM(S): 10090 
2013-00-00 | 2944066562 | PAXDB
ProteomicsM.musculus - Cell line, Cell line, SC (Menschaert,mcp,2013)
abundance based on Spectral counting, cell_line, Interaction consistency score: 3.6, Coverage: 43
ORGANISM(S): 10090 
2013-00-00 | 2956507553 | PAXDB
ProteomicsH.sapiens - Cell line, Hct116 (Koch,proteomics,2014)
abundance based on MAPPED_BY_AUTHORS, HCT116, Interaction consistency score: 4.6, Coverage: 5
ORGANISM(S): 9606 
2014-00-00 | 1430705385 | PAXDB
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