QPROT specifications

Information


Unique identifier OMICS_10677
Name QPROT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alexey Nesvizhskii <>

Publication for QPROT

QPROT in publications

 (7)
PMCID: 5423893
PMID: 28067236
DOI: 10.1038/ncomms14023

[…] for subsequent analysis., the peptide spectral counts of proteins were used to calculate fold change ratios and fdr p-values between gfp only, nes and nls samples using the qspec-param programme of qprot_v1.3.3 (ref. ). several criteria were used to classify proteins as being host-exposed proteins; no counts in the gfp only samples and an average greater than 2 peptides in the nes samples […]

PMCID: 5104757
PMID: 27891114
DOI: 10.3389/fmicb.2016.01757

[…] with the 26695 gene ids. if the protein was annotated with the same gene id in the p12 and nic25_a, respectively, the intensities were tested for differential abundance against each other with the qprot algorithm (). this was also used for identifying proteins uniquely abundant in each strain. the criterion set for this analysis was: protein found in at least 2 of 3 runs (triplicate analysis) […]

PMCID: 5016792
PMID: 27609711
DOI: 10.1038/srep33038

[…] proteins among the 3,990 mv, microparticle, and exosome proteins of the database., differentially expressed proteins (deps) between brain-extract—treated and control msc-mvs were identified using qprot software. control, untreated msc-mv proteome data were derived from our previous study. we defined deps as those with an fdr threshold of 0.01. to test the functional coherence of our findings, […]

PMCID: 4888286
PMID: 27257535
DOI: 10.7717/peerj.2007

[…] the principles of parsimony. for relative protein quantification of xylem sap from infected and non-infected plants, the qspec statistical framework (version 2, https://sourceforge.net/projects/qprot/) was used to assign significance to differentially regulated proteins, using a bayes factor >10 ()., nuclear magnetic resonance imaging (1h-mri) was done in an avance 400 spectrometer […]

PMCID: 5012864
PMID: 27472900
DOI: 10.7554/eLife.16220.036

[…] by deseq2., cell lysates from all 12 fibroblast cell lines were analyzed using somascan v4.0 according to manufacturer’s instructions and as previously reported (; ). data were analyzed using the qprot statistical package ()., the whole bone marrow was harvested from the long bones of dp16 mice (rrid:imsr_jax:013530) and matched littermate controls. cells were first purified using hemolysis […]


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QPROT institution(s)
Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Biostatistics, Rutgers University, NJ, USA; Department of Pathology, Yale University, CT, USA; Department of Pathology, University of Michigan Medical School, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, MI, USA

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