Mayu statistics

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Associated diseases

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Mayu specifications

Information


Unique identifier OMICS_18689
Name Mayu
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.08
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Ruedi Aebersold <>
  • person_outline Lukas Reiter <>

Additional information


Manual: http://proteomics.ethz.ch/muellelu/web/LukasReiter/Mayu/manual.html

Publication for Mayu

Mayu in publications

 (11)
PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] searched with x! tandem and comet against the annotated yeast proteins database with included reversed decoy peptides. search results were scored using peptideprophet and combined with iprophet. mayu was used to estimate iprophet probabilities to control for protein identification false discovery rate (fdr <1%). the final spectral library was assembled using spectrast by retaining spectra […]

PMCID: 5874767
PMID: 29401756
DOI: 10.3390/proteomes6010008

[…] modification. precursor and fragment mass tolerance were set to 20 ppm and 0.5 da, respectively, and 2 missed cleavages were allowed. false discovery rates at psm level and protein level using mayu [] were calculated, and protein identifications were obtained by applying the criteria of psm fdr < 1% and protein fdr < 1%. protein inference was performed using the panalyzer algorithm […]

PMCID: 5792000
PMID: 29385206
DOI: 10.1371/journal.pone.0192051

[…] a minimum protein probability of 0.9 was set to match a false discovery rate (fdr) of <1%. the resulting pep.xml and prot.xml files were used as input for the spectral counting software tool mayu []., fluorescence microscopy was used to visualize the c. acnes-induced platelet aggregates. c. acnes was added to prp as previously described. for c. acnes labeling dapi and oregon green […]

PMCID: 5663699
PMID: 29089484
DOI: 10.1038/s41467-017-01422-6

[…] mass spectrometric query parameters for 10,000 human proteins as prior information. we were able to reproducibly quantify 4056 unique proteins (swissprot identities, protein fdr = 0.01 controlled by mayu) across all samples. furthermore, we spiked heavy stable isotope-labeled peptide standards for 20 “anchor proteins” into the t1ds and t2n samples. this approach estimates the absolute abundances […]

PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398

[…] but also on the peptide- and protein-levels. this can be achieved, for example, by adapting a target-decoy approach as initially implemented for protein-level spectrum-centric analyses in mayu or recently in swath2stats. another option is the application of non-parametric modeling strategies for computing posterior probabilities at the peptide- and protein-level, as have been adapted […]


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Mayu institution(s)
Institute of Molecular Biology, University of Zurich, Zurich, Switzerland; Center for Model Organism Proteomes, University of Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland; Ph.D. Program in Molecular Life Sciences Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Institute of Computational Science, ETH Zurich, Zurich, Switzerland; Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland; Institute for Systems Biology, Seattle, WA, USA
Mayu funding source(s)
Supported, in whole or in part, by National Institutes of Health Contract N01-HV-28179 from the NHLBI; by grants from the Forschungskredit of the University of Zurich, the University of Zurich Research Priority Program in Systems Biology and Functional Genomics, the GEBERT-RUF Stiftung, Swiss National Science Foundation Grant 31000-10767, and SystemsX.ch, the Swiss initiative for systems biology.

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