Protein Prospector protocols

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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


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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 in pipelines

 (2)
2017
PMCID: 5320500
PMID: 28224978
DOI: 10.1038/srep42943

[…] 15n-metabolic labeling and mascot distiller quantitation was performed according to the protocol reported previously., the inter-crosslinked peptides were analyzed by batch-tag web database search (proteinprospector, university of california, san francisco). the mgf data were searched against the in-house database containing the sequences of 12 subunits of the pol v complex and 17 potential […]

2016
PMCID: 4976990
PMID: 27501389
DOI: 10.1371/journal.pone.0160536

[…] precursors, and in the second run, it was operated in targeted mode (tms2 mode). the list of precursors derived from the possible ubc9_ttr peptides with a glygly-tagged lysine was generated by the proteinprospector tool (http://prospector.ucsf.edu/prospector/mshome.htm). the ms/ms spectra were acquired in the orbitrap mass analyser with a resolution of 35,000 at m/z 200 with an isolation […]


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Protein Prospector in publications

 (92)
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 […]

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 […]

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 […]

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 […]

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 – […]


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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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