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QPROT specifications


Unique identifier OMICS_10677
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


No version available


  • person_outline Alexey Nesvizhskii

Publication for QPROT

QPROT citations


Identification of microsporidia host exposed proteins reveals a repertoire of rapidly evolving proteins

Nat Commun
PMCID: 5423893
PMID: 28067236
DOI: 10.1038/ncomms14023
call_split See protocol

[…] 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 or an […]


Cardiovascular proteomics in the era of big data: experimental and computational advances

PMCID: 5137214
PMID: 27980500
DOI: 10.1186/s12014-016-9124-y

[…] expression networks (Fig. ).Fig. 4 Improvements to computational methods that allow more robust results from label-free quantification are an area of active research. For example, recent works (e.g., QProt) have attempted to resolve the respective quantities of multiple proteins that share common peptide sequences in spectral counting, either using weighted average methods or more statistically mo […]


Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry Based Proteomics

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

[…] is 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) f […]


Microvesicles from brain extract—treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke

Sci Rep
PMCID: 5016792
PMID: 27609711
DOI: 10.1038/srep33038

[…] 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, […]


Sequence/structural analysis of xylem proteome emphasizes pathogenesis related proteins, chitinases and β 1, 3 glucanases as key players in grapevine defense against Xylella fastidiosa

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

[…] tisfy 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 equipped wi […]


Trisomy 21 consistently activates the interferon response

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

[…] 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 (). […]

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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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