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Protein Prospector specifications

Information


Unique identifier OMICS_12420
Name Protein Prospector
Alternative name ProteinProspector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format wml
Output format Qstar
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline ProteinProspector Team

Additional information


http://prospector.ucsf.edu/prospector/html/instruct/allman.htm

Information


Unique identifier OMICS_12420
Name Protein Prospector
Alternative name ProteinProspector
Interface Web user interface
Restrictions to use None
Input format xml
Output format Qstar
Computer skills Basic
Version 5.20.0
Stability Stable
Registration required Yes
Maintained Yes

Documentation


Maintainer


  • person_outline ProteinProspector Team

Additional information


http://prospector.ucsf.edu/prospector/html/instruct/allman.htm

Publications for Protein Prospector

Protein Prospector citations

 (179)
library_books

Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L

2018
Front Mol Biosci
PMCID: 5917446
PMID: 29725596
DOI: 10.3389/fmolb.2018.00040

[…] al., ). Mass spectrometry peak lists were generated using in-house software called PAVA. To identify peptide cleavage products, data searches were performed against the library of 228 peptides using Protein Prospector software (http://prospector.ucsf.edu/prospector/mshome.htm, UCSF). Because, in general, substrate binding pockets beyond four residues on each side of the scissile bond do not contr […]

library_books

A Toxin Antitoxin System VapBC15 from Synechocystis sp. PCC 6803 Shows Distinct Regulatory Features

2018
Genes
PMCID: 5924515
PMID: 29561797
DOI: 10.3390/genes9040173

[…] desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry analysis as previously described []. The predicted peptide fingerprint mass mappings of the co-purified proteins were obtained using ProteinProspector Tools (http://prospector.ucsf.edu/prospector/mshome.htm). Polyclonal antibodies were produced by immunizing New Zealand rabbit with the purified proteins []. […]

library_books

Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

2018
BMC Genomics
PMCID: 5859498
PMID: 29554870
DOI: 10.1186/s12864-018-4604-2

[…] siloxane (PCM) ion with m/z = 445.120025 was used for both MS and MS/MS scans [].Mass spectrometry centroid peak lists were generated using in-house software called PAVA, and data were searched using Protein Prospector software v. 5.19.1 []. Data were searched with carbamidomethylation of Cys as a fixed modification, and as variable modifications, oxidation of methionine, N-terminal pyroglutamate […]

library_books

Hydrogen peroxide positively regulates brassinosteroid signaling through oxidation of the BRASSINAZOLE RESISTANT1 transcription factor

2018
Nat Commun
PMCID: 5852159
PMID: 29540799
DOI: 10.1038/s41467-018-03463-x

[…] solution of 240,000, and MS2 scans were obtained from Orbitrap MS with a resolution of 30,000. The raw data from mass spectrometry was searched against the NCBI Arabidopsis protein database using the Protein Prospector searching software (http://prospector.ucsf.edu/prospector/mshome.htm), with a 10-ppm tolerance of the precursor and a 20-ppm tolerance for higher energy collision conditions (HCD) M […]

library_books

Salivary proteome profiling of oral squamous cell carcinoma in a Hungarian population

2018
FEBS Open Bio
PMCID: 5881539
PMID: 29632809
DOI: 10.1002/2211-5463.12391

[…] pava’ software were searched against the human subset of the UniProt database (downloaded on June 10, 2014; 136 245 target sequences concatenated with a randomized sequence for each entry) using the proteinprospector search engine (v.5.10.9.). Search parameters: enzyme: trypsin with maximum 1 missed cleavage site; fixed modification: carbamidomethyl (Cys); variable modifications: acetylation (pro […]

library_books

Harnessing insulin and leptin induced oxidation of PTP1B for therapeutic development

2018
Nat Commun
PMCID: 5773487
PMID: 29348454
DOI: 10.1038/s41467-017-02252-2

[…] from 0.1 to 1.0. Segments were compiled into single spectra, baseline corrected, and noise filtered using Data Explorer software (Applied Biosystems) and compared to in silico fragmentation using the Protein Prospector software (http://prospector.ucsf.edu/) (Supplementary Figs.  and ). […]

Citations

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Protein Prospector institution(s)
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
Protein Prospector funding source(s)
Supported by the Biomedical Technology Research Centers program of the NIGMS, National Institutes of Health (8P41GM103481).

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