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MASSyPup specifications


Unique identifier OMICS_02483
Name MASSyPup
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for MASSyPup

MASSyPup citations


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] tains a collection of data processing algorithms, a visualization framework, and metabolite annotation functions, while the plug-in for KNIME allows easy integration with other statistical workflows. MASSyPup [] does not actually integrate different procedures, but it does provide an easy platform for accessing many different tools in the form of a Linux distribution that can be run directly from […]


Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana

Front Plant Sci
PMCID: 5138414
PMID: 27999583
DOI: 10.3389/fpls.2016.01817

[…] verted to mzML file format using ProteoWizard (Kessner et al., ). The sum spectra were visualized in TOPPView (Sturm et al., ), a Gaussian noise filter (5 Da width) was applied to smooth the signals. MASSyPup64 and ESIprot were used as data processing platforms (Winkler, , ). […]


Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect resistant maize (Zea mays, p84C3) kernels by activity directed purification

Front Plant Sci
PMCID: 4553411
PMID: 26379694
DOI: 10.3389/fpls.2015.00670

[…] employed in this analysis both possible options, OMSSA version 2.1.9 win32 () and X!Tandem version ().We re-processed the mass spectrometry data with the Trans-Proteomic Pipeline 4.8.0 () on MASSyPup (). Raw files and results were deposited to the ProteomeXchange Consortium () via the PRIDE partner repository. The data may be accessed with the login [email protected] and password Td […]


Metabolic fingerprinting of Arabidopsis thaliana accessions

Front Plant Sci
PMCID: 4444734
PMID: 26074932
DOI: 10.3389/fpls.2015.00365

[…] atching were performed using SpiderMass (Winkler, ). The SpiderMass Meta-DB for Arabidopsis is provided as Supplemental Data . Mass spectrometry data processing was performed on the analysis platform MASSyPup (Winkler, ).Consensus features, HQ features and putative metabolite identifications with their compound classes were integrated into a SQLite ( database, which is availabl […]


An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64

PMCID: 4655102
PMID: 26618079
DOI: 10.7717/peerj.1401

[…] ; ; ).Thus, we compiled a computational platform for the high-throughput data analysis in proteomics and metabolomics, which facilitates the rapid set-up of workflows and the subsequent Data Mining. MASSyPup64 ( is a 64-bit live system, which can be run directly from external media. Open Source licenses of the software and the remastering utility provided on Fat […]


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MASSyPup institution(s)
Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Irapuato, Mexico

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