DebiChem Project
Summary
Analytical Biochemistry
DebiChem Analytical BioChemistry

This metapackage will install packages which enable you to:

  • load and convert mass spectrometric data files;
  • edit biopolymer sequences;
  • elaborate complex mass spectrometry workflows;
  • perform protein database searches using tandem-ms data;
  • visualize and explore mass spectrometric data;
  • simulate isotopic clusters;
  • implement proteomics workflows.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

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DebiChem Analytical Biochemistry packages

Official Debian packages with high relevance

comet-ms
Tandem mass spectrometry (MS/MS) search engine
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Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases.

This package ships a binary that does MS/MS database searches. Supported input formats are mzXML, mzML, and ms2 files. Supported output formats are .out, SQT, and pepXML.

Please cite: Jimmy K. Eng, Tahmina A. Jahan and Michael R. Hoopmann: Comet: an open source tandem mass spectrometry sequence database search tool. (PubMed) Proteomics 13(1) (2012)
freesasa
Solvent Accessible Surface Area of biomolecules
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FreeSASA is a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules. It is designed to be simple to use with defaults, but allows customization of all parameters of the calculation and provides a few different tools to analyze the results. Python bindings are provided separately.

Please cite: Mitternacht, Simon: FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189 (2016)
libmstoolkit-tools
libraries for manipulating mass spectrometry data - tools
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The MSToolkit is a light-weight C++ library for reading, writing, and manipulating mass spectrometry data. The MSToolkit is easily linked to virtually any C++ algorithm for simple, fast file reading and analysis.

Supported File Formats:

  • read-only mzML including internal compression (zlib and numpress) and external compression (.mzML.gz) read-only;
  • read-only mzXML including internal compression (zlib) and external compression (.mzXML.gz)
  • read/write mgf, ms1, ms2, bms1, bms2, cms1, cms2

Simple Interface:

  • Open any file format from a single function call;
  • Store any spectrum in a simple, comprehensive data structure;
  • Sequential or random-access file reading.

This package ships a MS/MS spectrum loader tool.

libpwiz-tools
ProteoWizard command line tools
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The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files.

This package ships command line tools that include idconvert (conversion of MS identifications) and msconvert (conversion of MS raw data files from/to any supported format).

lutefisk
de novo interpretation of peptide CID spectra
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Lutefisk performs a de novo interpreation of collision-induced decay (CID) spectra, providing the user with a file containing all the possible sequence candidates corresponding to the CID data.

massxpert
transitional package for massxpert -> massxpert2
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This is a transitional package. It can safely be removed. Runtime package.

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minexpert2
MS^n mass spectrometric data visualization and mining (runtime)
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mineXpert2 allows the user to perform the following tasks:

  • Open mass spectrometry data files (mzML, mzXML, asc, xy, ...);
  • Display in a table view the full data set, for easy filtering;
  • Calculate and display the TIC chromatogram;
  • Calculate and display a mz=f(rt) color map;
  • For mobility data, calculate and display a mz=f(dt) color map;
  • Integrate the mass spectrometric data from any kind of data representation (mass | drift spectra, TIC | XIC chromatogram, 2D color maps) to any other kind of data representation;
  • For any mass data feature (mass peak, TIC | XIC peak, color map) integrate to a XIC single intensity value;
  • Powerful isotopic cluster calculation starting from a chemical formula, optionally with user-defined isotopic abundance ratios;
  • Gaussian fit over any isotopic cluster to estimate the average mass of a given ion;
  • Mouse-driven deconvolution of m/z data (charge envelope-based or isotopic cluster-based);
  • Export the data to text files;
  • Export the graphical representation of mass spectrometric data to graphics files in a number of formats (jpg, png, pdf).

This package ships the mineXpert2 program.

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mmass
Mass spectrometry tool for proteomics
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mMass is a free mass spectrum viewer/analyzer in which the following proteomics-related tasks can be performed:

  • Open raw text, mzXML and mzData mass spectra;
  • Define peak lists;
  • Powerful mass spectrum viewer (zoom, cursor...);
  • Data recalibration;
  • Protein-only simulations;
  • Online Mascot searches.

The software can be easily extended by additional Python modules. This package contains the platform-independent parts of the software.

Please cite: Martin Strohalm, Daniel Kavan, Petr Novák, Michael Volný and Vladimír Havlíček: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. (PubMed,eprint) Analytical chemistry (ACS) 82(11):4648-4651 (2010)
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openms
package for LC/MS data management and analysis
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OpenMS is a package for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions.

TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of a set of numerous small applications that can be chained together to create analysis pipelines tailored for a specific problem.

This package is a metapackage that depends on both the libopenms library package (libOpenMS and libOpenMS_GUI) and the OpenMS Proteomic Pipeline (topp) package.

Please cite: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher: OpenMS – an Open-Source Software Framework for Mass Spectrometry. (PubMed,eprint) BMC Bioinformatics 9(163) (2008)
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python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
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python-pymzml (pymzML) is an extension to Python that offers:

  • easy access to mass spectrometry (MS) data that allows the rapid development of tools;
  • a very fast parser for mzML data, the standard in mass spectrometry data format;
  • a set of functions to compare or handle spectra.

This package contains python-pymzml for Python 3.

Please cite: T. Bald, J. Barth, A. Niehues, M. Specht, M. Hippler and C. Fufezan: pymzML - Python module for high throughput bioinformatics on mass spectrometry data. (PubMed,eprint) Bioinformatics, UK 28(7):1052-1053 (2012)
r-cran-maldiquant
GNU R package for quantitative analysis of mass spectrometry data
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MALDIquant provides a complete analysis pipeline for MALDI-TOF and other mass spectrometry data. Distinctive features include baseline subtraction using the SNIP algorithm, peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

Please cite: Sebastian Gibb and Korbinian Strimmer: MALDIquant: a versatile R package for the analysis of mass spectrometry data. (PubMed,eprint) Bioinformatics 28(17):2270-2271 (2012)
r-cran-maldiquantforeign
GNU R package providing import/export routines for MALDIquant
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The MALDIquantForeign package reads (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5) and writes (tab, csv, msd, mzML) different file formats of mass spectrometry data into/from MALDIquant objects.

r-cran-mixtools
GNU R tools for analyzing finite mixture models
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The GNU R mixtools package is a collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

Please cite: Tatiana Benaglia, Didier Chauveau, David R. Hunter and Derek Young: mixtools: An R Package for Analyzing Finite Mixture Models. (eprint) Journal of Statistical Software 32(6):1-29 (2009)
r-cran-readbrukerflexdata
GNU R package to read Bruker Daltonics *flex format files
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The readBrukerFlexData package reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series.

r-cran-readmzxmldata
GNU R package to read mass spectrometry data in mzXML format
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The readMzXmlData package contains functions for reading mass spectrometry data in mzXML format.

r-other-amsmercury
efficient calculation of accurate masses and abundances of isotopic peaks
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This GNU R package provides efficient calculation of accurate masses and abundances of isotopic peaks. It is a precondition for R NITPICK which does peak identification for mass spectrometry data.

r-other-curvefdp
estimation of confidence levels for peptide identifications
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This is a GNU R package for the Analytical Chemistry publication entitled 'Estimating the Confidence of Peptide Identifications without Decoy Databases'. The function curveFDR(scores) fits a gaussian mixture model to a score distribution of peptide identifications and thereby allows the estimation of confidence levels based on the false discvory proportion.

Please cite: Bernhard Y. Renard abd Wiebke Timm, Marc Kirchner, Judith A. J. Steen, Fred A. Hamprecht and Hanno Steen: Estimating the Confidence of Peptide Identifications without Decoy Databases. (eprint) Analytical Chemistry 82(11):4314-4318 (2010)
r-other-iwrlars
least angle regression, lasso, positive lasso and forward stagewise
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This GNU R package provides efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit. Least angle regression and infinitessimal forward stagewise regression are related to the lasso described in http://www-stat.stanford.edu/~hastie/Papers/#LARS.

This is a modified version of the original lars package by Hastie and Efron, providing a LARS modification for non-negative lasso.

r-other-nitpick
peak identification for mass spectrometry data
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This R package allows reliable extraction of features from mass spectra and helps in the automated analysis of proteomic mass spectrometry (MS) experiments.

This is the NITPICK implementation for peak picking in MS spectra.

Please cite: Bernhard Y Renard, Marc Kirchner, Hanno Steen, Judith AJ Steen and Fred A Hamprecht: NITPICK: peak identification for mass spectrometry data. (PubMed,eprint) BMC Bioinformatics 9:355 (2008)
tandem-mass
mass spectrometry software for protein identification
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X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification.

This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at http://www.thegpm.org/docs/X_series_output_form.pdf.

Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used.

toppic
Top-down proteoform identification and characterization (programs)
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The TopPIC Suite consists of four software tools for the interpretation of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.

 -TopFD (Top-down mass spectral Feature Detection) is a software tool
   for top-down spectral deconvolution and a successor to MS-Deconv.  It
   groups top-down spectral peaks into isotopomer envelopes and converts
   isotopomer envelopes to monoisotopic neutral masses. In addition, it
   extracts proteoform features from LC-MS or CE-MS data.
 -TopPIC (Top-down mass spectrometry based Proteoform Identification
   and Characterization) identifies and characterizes proteoforms at the
   proteome level by searching top-down tandem mass spectra against a
   protein sequence database. TopPIC is a successor to MS-Align+. It
   efficiently identifies proteoforms with unexpected alterations, such
   as mutations and post-translational modifications (PTMs), accurately
   estimates the statistical significance of identifications, and
   characterizes reported proteoforms with unknown mass shifts. It uses
   several techniques, such as indexes, spectral alignment, generation
   function methods, and the modification identification score (MIScore),
   to increase the speed, sensitivity, and accuracy.
 -TopMG (Top-down mass spectrometry based proteoform identification
   using Mass Graphs) is a software tool for identifying ultra-modified
   proteoforms by searching top-down tandem mass spectra against a
   protein sequence database.  It is capable of identifying proteoforms
   with multiple variable PTMs and unexpected alterations, such as
   histone proteoforms and phosphorylated ones.  It uses mass graphs,
   which efficiently represent candidate proteoforms with multiple
   variable PTMs, to increase the speed and sensitivity in proteoform
   identification. In addition, approximate spectrum-based filtering
   methods are employed for protein sequence filtering, and a Markov
   chain Monte Carlo method (TopMCMC) is used for estimating the
   statistical significance of identifications.
 -TopDiff (Top-down mass spectrometry-based identification of
   Differentially expressed proteoforms) compares the abundances of
   proteoforms and finds differentially expressed proteoforms by using
   identifications of top-down mass spectrometry data of several protein
   samples.
xtpcpp
Transitional package from xtpcpp to i2masschroq
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The program allows one to perform the following tasks:

 -Reads X!Tandem xml results files
 -Reads MASCOT dat results files
 -Reads TPP pepXML results files
 -Reads PSI mzIdentML results files
 -Run X!Tandem analyzes through a graphical user interface
 -Implements various filters based on statistical values
 -Powerful original grouping algorithm to filter redundancy
 -Phosphopeptide mode to handle phosphoproteomics datasets
 -Edit, search and sort the data graphically
 -XIC chromatogram browser (eXtracted Ion Current)
 -Comparisons of theoretical isotope patterns to measured MS1 XIC areas
 -Export data directly to Microsoft Office 2010 and LibreOffice (ods export)
 -Handle huge datasets very quickly
 -Perform peptide quantification through MassChroQml export

This package is a transitional package. You can remove it at any time.

Please cite: Olivier Langella, Benoît Valot, Thierry Balliau, Mélisande Blein-Nicolas, Ludovic Bonhomme and Michel Zivy: X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. (PubMed,eprint) Journal of Proteome Research 16(2):494-503 (2017)

Official Debian packages with lower relevance

libisospec++-dev
Isotopic fine structure calculator (C++ development files)
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IsoSpec implements an algorithm for fast computation of isotopologues of chemical substances that can alternate between joint probability and peak height threshold.

This package ships the development files.

Please cite: Mateusz K. Łącki, Michał Startek, Dirk Valkenborg and Anna Gambin: IsoSpec: Hyperfast Fine Structure Calculator. (PubMed,eprint) Analytical Chemistry 89(5):3272-3277 (2017)
libpwiz-dev
library to perform proteomics data analyses (devel files)
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The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files.

This package ships the library development files.

libpwizlite-dev
Library to load mzML/mzXML files (dev files)
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This library is a dumbed-down version of the Proteowizard library. This library only contains the required features to load standard mzML/mzXML mass spectrometry data files.

See http://proteowizard.sourceforge.net/ for the original project.

This package ships the development files.

Packaging has started and developers might try the packaging code in VCS

biceps
error-tolerant peptide identification
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BICEPS is tool for the error-tolerant identification of peptides based on a statistical regularization scheme. It balances possible improvements in peptide-spectrum-matches by allowing substitutions against the increased risk of false positives. BICEPS can identify peptides containing two or more substitutions as occuring e.g. in cross-species searches.

Please cite: Bernhard Y. Renard‡and Buote Xu, Marc Kirchner, Franziska Zickmann‡and Dominic Winter, Simone Korten‡and Norbert W. Brattig‡and Amit Tzur, Fred A. Hamprecht and Hanno Steen: Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS). (PubMed,eprint) Mol Cell Proteomics ;11(7):M111.014167 (2012)
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