Inspect protocols

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Inspect specifications

Information


Unique identifier OMICS_02397
Name Inspect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Inspect

Inspect in pipelines

 (3)
2015
PMCID: 4682130
PMID: 26674602
DOI: 10.1038/srep18311

[…] were analyzed using an ltq orbitrap xl mass spectrometer (thermo scientific, san jose, ca). mass spectra were searched using two different search algorithms, sequest (bioworks version 3.31 sp1) and inspect (version 20070905), with the rat refseq database (national center for biotechnology information, march, 2010, 30734 entries) which also included a list of common contaminating proteins […]

2012
PMCID: 3536893
PMID: 23082028
DOI: 10.1074/mcp.M112.019596

[…] using one or more of mascot 2.2 (), omssa 2.1.1 (), and tandem 2010.01.01.4 () with native, k-score 2010.01.01.4 (), and s-score 2010.01.01.4 pluggable scoring modules, myrimatch 1.5.8 (), and inspect 20110313 () with ms-gf spectral probability scoring (). it also combines the search results using an unsupervised machine-learning strategy and estimates peptide identification false […]

2012
PMCID: 3536893
PMID: 23082028
DOI: 10.1074/mcp.M112.019596

[…] database with a semi-tryptic search. to maximize search sensitivity, all peparml search engines were used: mascot; omssa; x!tandem with native, k-score, and s-score plugins; myrimatch; and inspect +ms-gf. amazon web-services elastic compute cloud (ec2) resources were used to supplement the local peparml computing resources to carry out this computationally intensive search on a total […]


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Inspect in publications

 (17)
PMCID: 5137872
PMID: 27918579
DOI: 10.1371/journal.pcbi.1005224

[…] in the metaproteomic sample. many peptide search engines have been developed for this purpose in the proteomics field, including commonly used tools such as mascot [], sequest [], x!tandem [], inspect [] and msgf+ []. their applications in metaproteomics rely on the pre-assembly of a protein database. early metaproteomic studies used the collection of proteins encoded by fully sequenced […]

PMCID: 4150949
PMID: 25124718
DOI: 10.1186/1475-2875-13-315

[…] 125,950 ms/ms spectra) were searched by peparml [] meta search engine. mascot 2.2 [], omssa 2.1.1 [], x!tandem 2010.01.01.4 [] with k-score 2010.01.01 [], and s-score 2010.01.01.4 plugins, inspect 20110313 [] and myrimatch 1.5.8 [] search engines were used within peparml with the following parameters: semi-specific trypsin digestion, one missed cleavage, precursor tolerance 10 ppm […]

PMCID: 4188997
PMID: 25056935
DOI: 10.1074/mcp.M114.040956

[…] engine (), which automatically conducts target and decoy searches using the following: mascot (), omssa (), and tandem () with native, k-score () and s-score pluggable scoring modules (), and inspect () with ms-gf spectral probability scoring (). the results were then combined using an unsupervised machine-learning strategy, and the peptide identification false discovery rates (fdr) […]

PMCID: 4006921
PMID: 24788524
DOI: 10.1371/journal.ppat.1004088

[…] controlled by the xcalibur data system (thermofinnigan). ms/ms spectra were extracted from the raw file with readw.exe (http://sourceforge.net/projects/sashimi). the ms/ms data were searched with inspect against the mgas315 streptococcus pyogenes database (nc_004070) with optional modifications: +15.9994 on methionine, +57.0214 on cysteine, and +79.9663 on threonine, serine, and tyrosine, […]

PMCID: 3873256
PMID: 24386107
DOI: 10.1371/journal.pone.0082655

[…] lc system (agilent technologies, santa clara, ca) connected to an ltq orbitrap velos mass spectrometer (thermo scientific, san jose, ca). spectra were matched to specific rat protein sequences using inspect , a “hybrid” algorithm that uses partial de novo sequencing combined with pattern matching. the raw data files were searched against a concatenated forward and reverse database that included […]


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Inspect institution(s)
Department of Bioengineering and Computer Science Department, University of California-San Diego, La Jolla, CA, USA

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