DebiChem Analytical Biochemistry packages

Comet est un moteur de recherche libre de base de données de séquences de spectrométrie de masse en tandem (MS/MS). Il identifie les peptides en recherchant dans les spectres MS/MS des séquences présentes dans les bases de données de séquences de protéines.

Ce paquet fournit un exécutable réalisant les recherches dans les bases de données MS/MS. Les formats de fichiers d'entrée pris en charge sont mzXML, mzML et ms2. Les formats de sortie pris en charge sont .out, SQT et pepXML.

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.

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.

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 réalise une interprétation de novo d’un spectre de CID (collision-induced decay – décomposition activée par une collision), donnant à l’utilisateur un fichier contenant toutes les séquences possibles correspondant aux données du CID.

Il s’agit d’un paquet de transition pouvant être supprimé sans danger.

MineXpert2 permet de réaliser les tâches suivantes :

 – ouvrir les fichiers de données de spectrométrie de masse (mzML, mzXML,
   asc, xy…) ;
 – afficher dans une table l’ensemble complet de données pour un
   filtrage aisé ;
 – calculer et afficher le chromatogramme TIC ;
 – calculer et afficher le graphique coloré mz=f(rt) ;
 – pour les données de mobilité, calculer et afficher la carte de
   couleurs mz=f(dt) ;
 – intégrer les données de spectrométrie de masse de n’importe quelle
   représentation de données (spectre de masse ou « drift »,
   chromatogramme TIC ou XIC, carte de couleurs 2D) dans n’importe
   quelle sorte de représentation ;
 – pour n’importe quelle caractéristique de masse (pic de masse, pic TIC
   ou XIC, carte de couleurs), intégrer dans une seule valeur
   d’intensité XIC ;
 – calcul puissant de groupe isotopique à partir d’une formule chimique,
   avec facultativement des ratios d’abondance définis par l’utilisateur ;
 – ajustement gaussien sur n’importe quel groupe isotopique pour estimer
   la masse moyenne d’une installation donnée ;
 – déconvolution avec la souris de données m/z (charge basée sur
   l’enveloppe ou sur le groupe isotopique) ;
 – exportation des données dans des fichiers texte ;
 – exportation de la représentation graphique de données de spectrométrie
   de masse dans des fichiers graphiques (jpg, png, pdf).

Ce paquet fournit le programme mineXpert2.

mMass est un analyseur et visualisateur de spectrométrie de masse, libre, avec lequel peuvent être réalisées les tâches suivantes relatives aux protéomes :

 — lecture des données de spectrométrie aux formats texte brut, mzXML
   et mzData ;
 — définition d’une liste de pics ;
 — visualisation de spectrométrie puissante (zoom, curseur…) ;
 — recalibration des données ;
 — simulation uniquement de protéines ;
 — recherche en ligne avec Mascot.

Ce logiciel peut être élargi facilement avec des modules supplémentaires en Python. Ce paquet fournit les parties indépendantes de l’architecture du logiciel.

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.

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.

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.

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.

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.

The readBrukerFlexData package reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series.

The readMzXmlData package contains functions for reading mass spectrometry data in mzXML format.

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.

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.

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.

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.

X! Tandem peut faire la correspondance de spectrométrie de masse en tandem avec des séquences de peptide, dans un processus qui est couramment utilisé pour réaliser l’identification de protéines.

Ce logiciel a une interface de programmation applicative (IPA) très simple et non sophistiquée : elle prend un fichier XML d’instructions sur sa ligne de commande et produit le résultat sous forme de fichier XML ayant été indiqué dans le fichier XML d’entrée. Le format de la sortie est décrit dans http://www.thegpm.org/docs/X_series_output_form.pdf.

Au contraire de quelques moteurs de recherche de générations précédentes, tous les moteurs des séries X! calculent la fiabilité statistique (valeurs espérées) pour toutes les affectations spectre-vers-séquence particulières. Ils réassemblent toutes les affectations de peptide dans un ensemble de données sur les séquences de protéine connues et affecte la fiabilité statistique de non aléatoirité de cet assemblage et alignement. La formule pour cela est disponible sur https://www.thegpm.org/docs/peptide_protein_expect.pdf. Par conséquent des logiciels d’assemblage et d’analyse statistique distincts, par exemple, PeptideProphet et ProteinProphet, n’ont pas besoin d’être utilisés.

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.

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

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.

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.

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.

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.