MASSyPup(64) - The Mass Spectrometry Live Linux


MASSyPup(64) is a Puppy Linux based Live distribution with is focused on the analysis of mass spectrometry data.

The system runs from DVD, USB and hard drive (with or without installation). The software is collected from free sources and may distributed with/ without data. It runs completely from RAM (if there is sufficient memory available) and therefore it is extremely fast.

The distribution contains many programs for mass spectrometry data conversion, data processing, mass spectrometry imaging (MSI), metabolomics and proteomics, such as (depending or release and version): ESIprot, imzML Converter, mmass, MZmine, OpenMZxy, OpenChrom, PepNovo, PeptideShaker, ProteoWizard tools (mscovert), R with XCMS and rJava, SearchGUI, SpiderMass, UniNovo, X!Tandem, X!Tandem Parser/ Viewer (see

The MASSyPup64 version is strongly focussed on efficient mass spectrometry data processing workflows and Data Mining and therefore contains the Workflow Management System taverna (Enterprise edition) and the R Data Mining GUI Rattle. For the concept of MASSyPup64, basic introduction into biological mass spectrometry data processing and application examples, please refer to the respective publication (open access).

Further, various programming languages and libraries are installed, such as: Java, Phython, Perl, g++, KDE/tk/tcl.. libraries, which facilitates the development and installation/ compilation of custom programs.

FNA - Frequently Needed Answers 64-bit MASSyPup: MASSyPup64

Q: Why you made a new MASSyPup version for 64-bit processors?
A: It is even more fast and some modern programs do not compile very well on 32-bit. Anyway, for most users the 64-bit version should give best performance. Another important issue is the fact that Puppy 32 does not boot from all Windows 8 UEFI systems. This is resolved now.

Q: Is MASSyPup64 also based on Puppy Linux?
A: MASSyPup64 is based on Fatdog64, a 64-bit relative of Puppy Linux.

Q: Does it contain the same software?
A: MASSyPup64 is more focussed on mass spectrometry data workflows, e.g. using taverna or TOPPAS. You find the list of included software this file.

FNA - Frequently Needed Answers 32-bit MASSyPup

Q: MASSyPup takes several minutes to boot. Is this normal?
A: Yes, especially the first boot takes a while, because all data are copied from the DVD into the RAM. However, once booted, The system is really fast!

Q: How can I install MASSyPup on a USB stick easily?
A: Download the .iso (link below) and create a bootable USB stick with UNetbootin (for Windows, Linux and Mac freely available).

Q: Where do I find the applications?
A: Please look in the Desktop folder "mass Apps". Note: Most programs work best, when started from a Console (X-Terminal).

Q: I run OpenMZxy. But where are the x/y data recorded?
A: The data are recorded as a .txt file In the main directory of the program. If you don't find the file there, you need go give write permissions to this directory (#chmod 777 -Rvf main) before running OpenMZxy.

Q: SpiderMass quits with "Error message: IOError: [Errno 2] No such file or directory: 'chemspider-token.txt' "
A: You need a Token for the ChemSpider Database. You can register free of charge at Then, you put your token in a simple text file called chemspider-token.txt in the SpiderMass directory (/usr/local/spidermass/main).

Q: Can I process the data on my hard drive, USB drive/ stick, ..?
A: Yes, you can mount physically connected media and process the data located there.

Q: Is it possible to install MASSyPup on my hard drive (e.g. containing Windows), USB drive/ stick, ..
A: Yes, please go to to the Puppy Linux page. Be careful! In general MASSyPup runs fine from DVD or USB.

Q; The Java program PeptideShaker, MZmine, .. does not start correctly.
A: The Java versions should be fine for the individual programs. However, sometimes the HEAP size is not determined correctly. You can fix this manually for your system, e.g.:
MZmine: In /usr/local/MZmine-2.10/
change HEAP_SIZE=`free -m | awk '/Mem:/ {print int($2 / 2)}'`
to HEAP_SIZE=2048
PeptideShaker: In /usr/local/PeptideShaker-0.22.6/resources/conf/JavaOptions.txt
change -Xmx****M
to -Xmx2048M

Q: Where do I find the Trans-Proteomic Pipeline (TPP)?
A: Open the Web Browser and go to http://localhost/tpp/cgi-bin/ Petunia will open and you can log in as 'guest' with/without any passwort.
A2: Version 2014/05/28: Open the Web Browser on the Desktop and click on "ISB/SPC Trans Proteomic Pipeline" ;-).

Q: How can I slim down/ remaster MASSyPup?
A: MASSyPup can be remastered with the included Puppy tools. E.g. You can erase some course data in /usr/local or put yours. For keeping the Trans-Proteomic Pipeline working, you have to copy the following files manually from /etc to /tmp/etc during the re-master process: passwd, group (I had to edit them manually for adding the www-data user) and the apache2 directory (which contains the Apache and TPP configuration). The welcome page is saved at /usr/share/doc/home.htm and also must be copied manually.

Change Log

2016-12-07: MASSyPup64 moved to Zenodo:

2016-1-26: If you are using the MSI.R scripts for analyzing mass spectrometry images, please upgrade from our git repository (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).


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,


MASSyPup64: All files are deposited at Zenodo: You can install the ISO file on an USB-stick (recommended), e.g. using Rufus.

MASSyPup (old 32bit-version): The 32-bit MASSyPup (depreciated) ISO DVD image can be downloaded from Zenodo (.iso files without '64'):


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