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Qvality specifications

Information


Unique identifier OMICS_15889
Name Qvality
Interface Web user interface
Restrictions to use None
Input data The empirical score distribution and a corresponding N/A score distribution or only the empirical p-value distribution.
Programming languages C++
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Lukas Kall

Information


Unique identifier OMICS_15889
Name Qvality
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The empirical score distribution and a corresponding N/A score distribution or only the empirical p-value distribution.
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Lukas Kall

Publication for Qvality

Qvality citations

 (9)
library_books

SuperQuant assisted comparative proteome analysis of glioblastoma subpopulations allows for identification of potential novel therapeutic targets and cell markers

2018
Oncotarget
PMCID: 5823648
PMID: 29507698
DOI: 10.18632/oncotarget.24321

[…] 05 [], with the standard feature set. All PSMs with q-value < 0.01 were grouped together using sequence and theoretical mass, and the highest Percolator SVM score was used as the score for the group. Qvality 2.05 [] was used for the estimation of q-value on the PSM group level, PSM groups were filtered by q-value < 0.01. Each PSM group gives rise to one peptide. Proteins related to the filtered pe […]

library_books

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

2017
Front Microbiol
PMCID: 5474472
PMID: 28674527
DOI: 10.3389/fmicb.2017.01127

[…] All statistical analyses were performed using Primer6+ () and the R software (). Adjustments for multiple testing were performed using the false discovery rate correction according to performed with qvality () unless indicated otherwise. We tested the effect of the following factors: tillage regime with conventional (CT) and reduced (RT) tillage, crop residue management with residue retention (R+ […]

library_books

Inference and quantification of peptidoforms in large sample cohorts by SWATH MS

2017
Nat Biotechnol
PMCID: 5593115
PMID: 28604659
DOI: 10.1038/nbt.3908

[…] rosenberger/pyprophet/tree/feature/ipf @93ec307) was run on a concatenated file of all 13 runs containing only the unambiguous phosphopeptides with the following parameters:--final_statistics.emp_p --qvality.enable --qvality.generalized--ms1_scoring.enable --uis_scoring.enable--semi_supervised_learner.num_iter=20 --xeval.num_iter=20--ignore.invalid_score_columns.PyProphet in site-localization mode […]

library_books

Spatiotemporal control of interferon induced JAK/STAT signalling and gene transcription by the retromer complex

2016
Nat Commun
PMCID: 5150223
PMID: 27917878
DOI: 10.1038/ncomms13476

[…] resulting Mascot result files were further processed by using myProMS and the estimated false discovery rate by automatically filtering the Mascot score of all peptide identifications was set to 1% (Qvality). […]

library_books

The impact of sequence database choice on metaproteomic results in gut microbiota studies

2016
Microbiome
PMCID: 5037606
PMID: 27671352
DOI: 10.1186/s40168-016-0196-8

[…] hermo Scientific). For MPA analysis, X!Tandem [] was used as search engine (precursor ion tolerance 10 ppm, fragment ion tolerance 0.02 Da, max missed cleavages 2, plus default search parameters) and qvality [] as validation tool. For MQ analysis, carbamidomethylation of cysteine was set as fixed modification and oxidation of methionine as variable modification, and the other parameters were set a […]

library_books

Distinct soil microbial diversity under long term organic and conventional farming

2014
PMCID: 4409162
PMID: 25350160
DOI: 10.1038/ismej.2014.210

[…] is was peformed in GINKGO () with 105 permutations. P-value adjustments for multiple comparisons were performed using the false discovery rate correction according to . Q-values were determined using QVALITY () and associations were considered significant at q<0.05. Singletons and doubletons, that is, OTUs that were represented by only one or two sequences across the whole data set, hold little in […]

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Qvality funding source(s)
This work was funded by NIH awards R01 EB007057 and P41 RR11823.

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