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MASSyPup(64) - The Mass Spectrometry Live Linux

 

MASSyPup(64) is a Linux Live distribution for the analysis of mass spectrometry data. It can be run directly from a USB drive, or installed on a hard disc. Further, it is possible to remaster MASSyPup(64), for distributing software and/ or datasets, e.g. for training courses.

 

Software list (version 20190525_mp64_docker)

High-level programming languages

Program Description Call References
Docker DevOps/ Containerisation docker https://www.docker.com/
OpenJDK Open Java Development Kit java https://openjdk.java.net/
Python 2 and 3 Python programming language python/ python3 https://www.python.org/

 

General MS programs

Program Description Call References
ESIprot molecular weight determination from multiply charged ions esiprot http://www.bioprocess.org/esiprot/
mMass versatile MS tool mmass http://mmass.org/
MZmine 2 MS data processing (mainly LC-MS) mzmine http://mzmine.github.io/

 

For ESIprot, example data are installed in /usr/local/mp64.

R packages and tools

Program Description Call References
CRAN R recent version of R R https://www.r-project.org/
RStudio (Integrated Development Environmet) rstudio https://www.rstudio.com/
MALDIquantForeign reading/ writing of MS data R>library(MALDIquantForeign) http://www.strimmerlab.org/software/maldiquant/
MALDIquant quantitative analysis of MS data R>library(MALDIquant) http://www.strimmerlab.org/software/maldiquant/
MetaboAnalystR (metabolomics data processing) R>library(MetaboAnalystR) https://github.com/xia-lab/MetaboAnalystR
XCMS (LC-MS data processing) R>library(xcms) https://bioconductor.org/packages/release/bioc/html/xcms.html
RmsiGUI (Mass Spectrometry Imaging platform) R>library(RmsiGUI) https://bitbucket.org/lababi/rmsigui
Rattle Data Mining GUI for R R>library(rattle) https://rattle.togaware.com/

 

The Graphical User Interface (GUI) of the Trans-Proteomic Pipeline - Petunia http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP can be run as a Docker image. Running Docker requires root access (sudo su; password "mp64"):

 docker run -dit --user=root -p 10401:10401 -v /tmp/tppdata:/data spctools/tpp apache2ctl -DFOREGROUND 

After starting the container, Petunia is available from a web browser at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl. To login, one can use the login "guest" with password "guest".

Change Log

2019-05-25: New version, based on antiX, and including Docker. Available from https://zenodo.org/record/3228788. Direct download link: https://zenodo.org/record/3228788/files/20190525_mp64_docker.iso?download=1

2016-12-07: MASSyPup64 moved to Zenodo: http://doi.org/10.5281/zenodo.195529

2016-1-26: If you are using the MSI.R scripts for analyzing mass spectrometry images, please upgrade from our git repository https://bitbucket.org/lababi/msi.r (git clone https://This email address is being protected from spambots. You need JavaScript enabled to view it./lababi/msi.r.git). 

2015-11-26: Installation of Mass-Up for MALDI-ToF data analyses (pre-processing, clustering etc.). Seems to work fine for metabolic fingerprinting data as well! Reference: H. López-Fernández et al., BMC Bioinformatics, 2015.

2015-11-17: Open access article: Winkler (2015), An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PeerJ 3:e1401; DOI 10.7717/peerj.1401

2015-11-13: RKWard, an excellent GUI for R, is included now. Since I had to compile KDE, I also added the Calligra office suite, which contains a word processor, a spreadsheet program, a presentation program, a visual database management front-end, a project management application, a notetaking and mindmapping application, a  flowchart drawing program, a  vector graphics editor, a digital painting program and an e-book authoring application. Further, R was upgraded to 3.2.0 and a basic LaTeX installation was included (with editor Kile). 

2015-09-04: Bug fixes, inclusion of examples for Proteomics and Metabolomics (targeted and un-targeted). Several workflows were included for protein identification and validation (with extraction of proteins of interest; text mining; optimized and implemented in taverna) and LC-MS data processing for untargeted Metabolomics (feature finding, alignment, text export, adjusted from the OpenMS/TOPPAS examples). TPP 4.8 and some special tools for large data editing were add: The non-conventional spreadsheet program teapot and a command line program for transposing large matrices.

2015-06-17: First version of MASSyPup64 (link to .iso), based on Fatdog64.

2015-02-27: Installation of R packages MALDIquant and MALDIquantForeign, for MS data analysis in R. Upgrade of SpiderMass. Inclusion of a low-temperature plasma (LTP) mass spectrometry imaging (MSI) data set of chili pepper (as reported in Maldonado et al., 2014, Journal of Proteomics). Installation of MSI.R scripts for MSI data analysis with R. Unetbootin installed for Live-USB stick creation.

2014-09-04: Inclusion of RMassBank for the generation of high-quality entries. MM14 data set for the testing/ optimization of algorithms added. Upgrade of MZmine to version 2.11 (including GridMass) and upgrade of the Trans-Proteomic Pipeline to version 4.7.1. Inclusion of an R script for converting cdf files to mzData (other conversions can be done by msconvert).

2014-05-28: DeNovoGUI added, SearchGUI and PeptideShaker updated. Buffer overflow problem of Comet fixed (many thanks to Jimmy K. Eng!). Various Perl scripts in TPP corrected (#!/usr/bin/perl). TPP now is accessible directly after starting the Web Browser, with Comet as the default search engine.

2014-05-19: OpenMS/TOPP (TOPPAS/ TOPPView) and Comet added.

2014-03-13: Trans-Proteomic Pipeline (TPP) added. Upgrade of SpiderMass.

2014-02-01: metaXCMS added. Upgrade of SpiderMass (formula generator and isotope calculator).

Reference

If MASSyPup is useful for you, please cite:

Winkler R.: An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PeerJ, 3:e1401, 1-34, 2015, DOI 10.7717/peerj.1401

Winkler R.: MASSyPup – an 'Out of the Box' solution for the analysis of mass spectrometry data. Journal of Mass Spectrometry, 49(1), 37-42, 2014,  http://dx.doi.org/10.1002/jms.3314

Download

MASSyPup64: All files are deposited at Zenodo: https://zenodo.org/record/3228788 You can install the ISO file on an USB-stick (recommended), e.g. using Rufus. The recommended version is https://www.zenodo.org/record/3228788/files/20190525_mp64_docker.iso?download=1

MASSyPup (old 32bit-version): The 32-bit MASSyPup (depreciated) ISO DVD image can be downloaded from Zenodo (.iso files without '64'): http://doi.org/10.5281/zenodo.195529.

Installation

 1) Create a bootable USB stick from the iso, e.g. using:

2) Then re-boot your computer, and select booting from USB storage device.(e.g. [F9], change boot order)

Contact

Please send any questions, comments, suggestions to This email address is being protected from spambots. You need JavaScript enabled to view it..