DTASelect protocols

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DTASelect specifications

Information


Unique identifier OMICS_09160
Name DTASelect
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for DTASelect

DTASelect in pipelines

 (2)
2011
PMCID: 3223167
PMID: 22132090
DOI: 10.1371/journal.pone.0027173

[…] where nrev is the number of peptides identified from the reverse database and nreal is the number of peptides identified from the real (forward) database ., peptides obtained from our sequest/dtaselect searches were searched against the 6b and 16b protein databases using fasts and against raw sequencing reads using tfasts , using an e-value cutoff of 10-5., pepnovo+ and peaks algorithms […]

2011
PMCID: 3223167
PMID: 22132090
DOI: 10.1371/journal.pone.0027173

[…] if a psm does not have at least 3 residues within a peptide sequence string that match two or more algorithms, that spectrum would be considered unique to that algorithm. the identified sequest/dtaselect psms for rmps-6a and -6b sequence databases with a 1-peptide minimum and deltcn of 0.00 for 6a (run 2 and 3) and 6b (run 1 and 2) were compared to the psms from peaks and pepnovo+. […]


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DTASelect in publications

 (216)
PMCID: 5949005
PMID: 29686080
DOI: 10.1073/pnas.1802354115

[…] peptides in the search with no consideration for missed cleavages; and (iv) static modification of +57.02156 on cysteine residues. peptide identifications were organized and filtered by using the dtaselect algorithm, which uses a linear discriminant analysis to identify peptide-scoring thresholds that yield a peptide-level fdr of <5% as estimated by using a decoy database approach. […]

PMCID: 5870951
PMID: 29584760
DOI: 10.1371/journal.pone.0194518

[…] filtered to 10-ppm, and 50-ppm fragment ion tolerance with a maximum of two internal missed cleavages using the custom databases. identified spectra were filtered and grouped into proteins using dtaselect. proteins and microproteins required, at least, one peptide to be identified with a setting of less than 1% fdr., to identify microproteins, data files from technical duplicates […]

PMCID: 5856802
PMID: 29549327
DOI: 10.1038/s41598-018-23090-2

[…] and light labels (+8.0444), were considered as metabolic labelling. data was searched with 50 ppm precursor ion tolerance and 600 ppm fragment ion tolerance. identified proteins were filtered using dtaselect. filtering required a minimum of 2 peptides per protein, at least one tryptic terminus for each peptide, and less than 1% fdr. normalised spectral abundance factor (nsaf) was calculated […]

PMCID: 5834214
PMID: 29462184
DOI: 10.1371/journal.ppat.1006892

[…] protein and peptide identification were performed with integrated proteomics pipeline—ip2 (integrated proteomics applications, san diego, ca. http://www.integratedproteomics.com/) using prolucid and dtaselect2 algorithms. dtaselect parameters were—p 2 -y 1—trypstat—pfp .01 –extra-pi-db-dm-in. spectrum raw files were extracted into ms2 files from raw files using open source rawextract 1.9.9 […]

PMCID: 5810618
PMID: 29441361
DOI: 10.1126/sciadv.aao3424

[…] melanogaster and d. simulans uniprotkb protein database (04_2014), which included the reverse sequences of both species-specific databases to allow determination of an fdr at the peptide level with dtaselect2 (). search results were uploaded to ip2 (integrated proteomics solutions), and high-resolution ms/ms mass spectra were used to quantify relative protein expression based on isobaric […]


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DTASelect institution(s)
Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA; Scripps Research Institute, Department of Cell Biology, La Jolla, CA, USA

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