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Protocols

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

 (93)
library_books

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

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

[…] (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 []., assay […]

library_books

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

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

[…] the hhv-6b protein database was searched initially allowing for two missed and one non-specific cleavage to allow for peptides with alternative splicing or unpredicted start/stop sites. standard protein prospector scores (minimum protein score 22, minimum peptide score 15, maximum protein expectation value 0.01 and maximum peptide expectation value 0.001) produced a 5% fdr for protein […]

library_books

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

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

[…] 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 […]

library_books

Targeting RAS driven human cancer cells with antibodies to upregulated and essential cell surface proteins

2018
PMCID: 5796798
PMID: 29359686
DOI: 10.7554/eLife.31098.027

[…] time of 60 ms with a normalized collision energy at 27, and an isolation window of 1.5 m/z with an isolation offset of 0.5 m/z., peptide search and ms1 peak area quantification were performed using proteinprospector (v.5.13.2) against 20203 human proteins (swiss-prot database, obtained march 5, 2015) with a false discovery rate of 1%., quantitative data analysis was performed using a customized […]

library_books

Coevolving MAPK and PID phosphosites indicate an ancient environmental control of PIN auxin transporters in land plants

2017
PMCID: 5814726
PMID: 29197077
DOI: 10.1002/1873-3468.12929

[…] the ms/ms data by the proteome discoverer software (v. 1.4.1.14; thermo fisher scientific) were searched against the swissprot database (downloaded 12/14/2015, 550116 target sequences) using the proteinprospector search engine (v.5.18.0.). search parameters: enzyme – trypsin with maximum 1 missed cleavage per peptide; fixed modification – carbamidomethyl (cys); variable modifications – […]

library_books

Combined Venom Gland Transcriptomic and Venom Peptidomic Analysis of the Predatory Ant Odontomachus monticola

2017
PMCID: 5666370
PMID: 29027956
DOI: 10.3390/toxins9100323

[…] the mass-to-charge ratios for multiple charged ions were deconvoluted to give molecular masses. peptide sequences were manually determined from ms/ms spectra and were confirmed by ms-product in proteinprospector program []., we thank toshiyuki sato (tokyo university of agriculture and technology), mamoru terayama (university of tokyo), katsuyuki eguchi (tokyo metropolitan university), […]


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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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