DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics.

By David L. Tabb, McDonald Wh, Y. rd. Journal of Proteome Research, 2002

1,396 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/630a76403459e7163b4a629cbd4936b951aec8de

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Citations in the corpus

A method for the comprehensive proteomic analysis of membrane proteins (2003, methodology): “DTASelect then assembled the peptide sequences into proteins and removed redundant protein sequence”
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: a Strike Against Decoy Databases (2008, background): “55 × 10−8 are actually more statistically significant than some proteins with multiple peptide hits but larger SpectralP robability values (see [48,49,50,44] for combining peptide significance scores into protein significance scores).”
Interpretation of Shotgun Proteomic Data (2005, methodology): “DTASelect (39) is another widely used tool for processing of shotgun proteomic data.”
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. (2004, methodology): “To institute such file format changes we made modifications to several pre– search (extraction and filtering), searching (SEQUEST), organization and summary (DTASelect, Tabb et al. 2002), and visualization (results display) programs.”
Wnt proteins are lipid-modified and can act as stem cell growth factors (2003, methodology): “Search results were filtered and grouped using the DTASelect progra”
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. (2005, methodology): “The program CONTRAST was used to compare peptides etween protein complexes (Tabb et al., 2002). orthern Analysis east Strains were grown at 30°C and 39°C in YP+ 2% dextrose or P+ 2% galactose with 20 ug/ml of adenine.”
Correlative GC-TOF-MS-based metabolite profiling and LC-MS-based protein profiling reveal time-related systemic regulation of metabolite–protein networks and improve pattern recognition for multiple biomarker selection (2005, methodology): “For quantitative analysis, CONTRAST was used to compare identified proteins and peptides from different runs (Tabb et al., 2002).”
Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus (2012, neutral): “ProLuCID search results were then filtered with DTA Select 2.0 (Tabb et al., 2002) using a cutoff of 1% for peptide false identification rate (-fp 0.01).”