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mMass specifications


Unique identifier OMICS_03357
Name mMass
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Martin Strohalm

Publication for mMass

mMass citations


An Extended Eddy‐Diffusivity Mass‐Flux Scheme for Unified Representation of Subgrid‐Scale Turbulence and Convection

PMCID: 5947327
PMID: 29780442
DOI: 10.1002/2017MS001162

[…] pointing vertical unit factor.κvon kármán constant ( κ=0.41).llatent heat of vaporization.λmonin‐obukhov length.leddy mixing length.leinternal eddy mixing length.lssurface‐based eddy mixing length.mmass flux.ptotal pressure.〈ph〉domain‐mean hydrostatic pressure.p†departure of pressure from domain‐mean hydrostatic pressure.qlliquid water specific humidity.qssaturation specific humidity.qttotal […]


Spatial Systems Lipidomics Reveals Nonalcoholic Fatty Liver Disease Heterogeneity

Anal Chem
PMCID: 5906754
PMID: 29570976
DOI: 10.1021/acs.analchem.7b05215

[…] then imported to scils software v.2016a (scils, bremen, germany) where they were together normalized by total ion count. the overall mean spectrum from all 23 samples was extracted and exported to mmass v.5.5 where it was subjected to autoscaling, baseline subtraction, and smoothing (gaussian algorithm with window size of 0.1 m/z and 2 cycles). peak picking was performed on the spectrum […]


Dynamics of Scabin toxin. A proposal for the binding mode of the DNA substrate

PLoS One
PMCID: 5854381
PMID: 29543870
DOI: 10.1371/journal.pone.0194425

[…] the cases where peptides were overlapping, spectra were collected using ion-mobility spectrometry to separate peptides based on their size, shape and charge., digested peptides were identified using mmass [] and corresponding masses were analyzed using the findpept tool on the expasy proteomics server (mass tolerance ± 0.5 da) to determine peptide sequences. peptides that could not be confirmed […]


Lipids Shape the Electron Acceptor Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

Cell Chem Biol
PMCID: 5856493
PMID: 29358052
DOI: 10.1016/j.chembiol.2017.12.012

[…] a high mass mode acquisition window of 1000-6000 m/z and an agc target of 1 000 000. data were analysed using the xcalibur 3.0 (thermo scientific, waltham, ma), unidec ( and mmass software packages ( (, ). the appearance of dhodh in the mass spectra was invariant between different protein preparations and could be reproduced by using […]


Schistosoma mansoni SmKI 1 serine protease inhibitor binds to elastase and impairs neutrophil function and inflammation

PLoS Pathog
PMCID: 5823468
PMID: 29425229
DOI: 10.1371/journal.ppat.1006870

[…] in milli-q h2o, mixed to a saturated solution of α-cyano-4-hydroxycinnaminic acid, spotted on a maldi sample plate, and dried at room temperature. all resulting data was analyzed manually using both mmass and flex analysis 3.0 (bruker daltonics) softwares. also, the secondary structure of the refolded protein was investigated by circular dichroism using a jasco-j815 spectropolarimeter (jasco […]


Outer Membrane Vesicle Vaccines from Biosafe Surrogates Prevent Acute Lethal Glanders in Mice

PMCID: 5874646
PMID: 29320408
DOI: 10.3390/vaccines6010005

[…] laser intensity of 2500 to accumulate 1000 shots/spectrum across the mass range of 1200–1900 da. acquired spectra t2d files were converted to mzxml files and further analyzed on the open source mmass software. three independently isolated lipid a samples had their mass scans normalized and averaged for the spectrums presented., select agent animal work was performed in a cdc/usda tier 1 […]

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mMass institution(s)
Institute of Microbiology, Academy of Sciences of the Czech Republic, vvi; Videnska, Prague, Czech Republic

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