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Mayu specifications


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




No version available


  • person_outline Ruedi Aebersold
  • person_outline Lukas Reiter

Additional information


Publication for Mayu

Mayu citations


Cost effective generation of precise label free quantitative proteomes in high throughput by microLC and data independent acquisition

Sci Rep
PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] were 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 abo […]


In Depth Proteomic Characterization of Classical and Non Classical Monocyte Subsets

PMCID: 5874767
PMID: 29401756
DOI: 10.3390/proteomes6010008

[…] riable 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 []. Thos […]


Platelet activation and aggregation by the opportunistic pathogen Cutibacterium (Propionibacterium) acnes

PLoS One
PMCID: 5792000
PMID: 29385206
DOI: 10.1371/journal.pone.0192051
call_split See protocol

[…] rtex)[]. 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 []. […]


Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

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

[…] eeds specific attention when the large, external spectral libraries are used in targeted proteomics. Therefore, to pursue a strict quality control of protein-level identification, we further utilized Mayu software, which computed and applied an m_score cutoff of 0.00000218972 at the peptide peak group level to achieve the protein FDR of 1% in our final result. Using an in-house script, the signal […]


Statistical control of peptide and protein error rates in large scale targeted DIA analyses

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

[…] uery-level, 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 f […]


Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process

BMC Genomics
PMCID: 5374549
PMID: 28361671
DOI: 10.1186/s12864-017-3491-2
call_split See protocol

[…] olator-converters (v3-00) followed by percolator (v2-08) for further quality control. The percolator tools can be downloaded from ( []. In this study, we used MAYU for protein assembling []. Peptides less than 7 amino acids were not taken into account. […]


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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, the Swiss initiative for systems biology.

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