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Protocols

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

Versioning


No version available

Publication for Inspect

Inspect citations

 (36)
library_books

A Graph Centric Approach for Metagenome Guided Peptide and Protein Identification in Metaproteomics

2016
PLoS Comput Biol
PMCID: 5137872
PMID: 27918579
DOI: 10.1371/journal.pcbi.1005224

[…] resent 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 bac […]

library_books

Autophagic degradation of aquaporin 2 is an early event in hypokalemia induced nephrogenic diabetes insipidus

2015
Sci Rep
PMCID: 4682130
PMID: 26674602
DOI: 10.1038/srep18311

[…] s 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 from ot […]

call_split

The Pilus Usher Controls Protein Interactions via Domain Masking and is Functional as an Oligomer

2015
PMCID: 4496297
PMID: 26052892
DOI: 10.1038/nsmb.3044
call_split See protocol

[…] (http://sourceforge.net/projects/sashimi). The resulting mzXML file contains all the data for all MS/MS spectra and can be read by the subsequent analysis software. The MS/MS data were searched using InsPecT and GPM X!Tandem against the Ecoli_K12 UniProt database (downloaded 3/19/2013) with optional modifications: +16 on Methionine, +57 on Cysteine, and +80 on Threonine, Serine and Tyrosine. Only […]

library_books

Universal database search tool for proteomics

2014
Nat Commun
PMCID: 5036525
PMID: 25358478
DOI: 10.1038/ncomms6277

[…] Low, Phosphorylation, Trypsin) [] (). Interestingly, without phosphorylation-specific scoring parameters, MS-GF+ outperformed both tools, identifying 37% and 44% more PSMs than Mascot+Percolator and InsPecT, respectively. With phosphorylation-specific parameters, MS-GF+ identified 9% more PSMs (and 12% more PSMs of phosphopeptides), confirming that our scoring model successfully captures phosphor […]

library_books

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility

2014
Malar J
PMCID: 4150949
PMID: 25124718
DOI: 10.1186/1475-2875-13-315

[…] metesRep3: 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 and f […]

library_books

Sex partitioning of the Plasmodium falciparum Stage V Gametocyte Proteome Provides Insight into falciparum specific Cell Biology*

2014
PMCID: 4188997
PMID: 25056935
DOI: 10.1074/mcp.M114.040956

[…] asearch 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) were e […]


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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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