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
Links to other tasks
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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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Versions of package comet-ms |
Release | Version | Architectures |
bookworm | 2019015+cleaned1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2019015+cleaned1-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2018012-1 | amd64,arm64,armhf,i386 |
stretch | 2014022-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 2019015+cleaned1-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2019015+cleaned1-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2021010 |
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License: DFSG free
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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.
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freesasa
Solvent Accessible Surface Area of biomolecules
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Versions of package freesasa |
Release | Version | Architectures |
trixie | 2.1.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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libmstoolkit-tools
libraries for manipulating mass spectrometry data - tools
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Versions of package libmstoolkit-tools |
Release | Version | Architectures |
bookworm | 82-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 82-7.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 82-6 | amd64,arm64,armhf,i386 |
bullseye | 82-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 82-7.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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libpwiz-tools
ProteoWizard command line tools
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Versions of package libpwiz-tools |
Release | Version | Architectures |
jessie | 3.0.6585-2 | amd64,armel,armhf,i386 |
sid | 3.0.18342-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.0.18342-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.18342-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.18342-2 | amd64,arm64,armhf,i386 |
stretch | 3.0.9393-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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).
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lutefisk
de novo interpretation of peptide CID spectra
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Versions of package lutefisk |
Release | Version | Architectures |
bullseye | 1.0.7+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.7+dfsg-4 | amd64,arm64,armhf,i386 |
stretch | 1.0.7+dfsg-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.7+dfsg-4 | amd64,armel,armhf,i386 |
bookworm | 1.0.7+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.0.7+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.0.7+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package lutefisk: |
field | biology, chemistry |
role | program |
science | calculation |
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License: DFSG free
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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.
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massxpert
transitional package for massxpert -> massxpert2
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Versions of package massxpert |
Release | Version | Architectures |
sid | 8.5.0-1 | all |
bullseye | 6.0.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 7.0.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.6.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 8.5.0-1 | all |
jessie | 3.4.1-1 | amd64,armel,armhf,i386 |
Debtags of package massxpert: |
biology | nuceleic-acids, peptidic |
field | biology, chemistry |
interface | x11 |
role | program |
uitoolkit | qt |
use | analysing, simulating |
works-with | biological-sequence |
works-with-format | xml |
x11 | application |
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License: DFSG free
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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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Versions of package minexpert2 |
Release | Version | Architectures |
bullseye | 7.4.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 8.6.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 9.6.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 9.6.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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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Versions of package mmass |
Release | Version | Architectures |
stretch | 5.5.0-5 | all |
buster | 5.5.0-5 | all |
jessie | 5.5.0-4 | all |
Debtags of package mmass: |
field | biology, chemistry |
interface | x11 |
role | program |
science | plotting, visualisation |
scope | application |
uitoolkit | gtk, wxwidgets |
use | analysing |
works-with | biological-sequence, db |
works-with-format | xml |
x11 | application |
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License: DFSG free
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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.
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openms
Paket für Verwaltung und Analyse von LC/MS-Daten
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Versions of package openms |
Release | Version | Architectures |
buster | 2.4.0-real-1 | all |
bullseye | 2.6.0+cleaned1-3 | all |
bookworm | 2.6.0+cleaned1-3 | all |
trixie | 2.6.0+cleaned1-4 | all |
sid | 2.6.0+cleaned1-4 | all |
jessie | 1.11.1-5 | all |
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License: DFSG free
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OpenMS ist ein Paket für Verwaltung und Analyse von LC/MS-Daten. OpenMS
bietet Infrastruktur für die Entwicklung von massenspektrometrie-bezogene
Software und leistungsfähige 2D- und 3D-Visualisierungen.
TOPP (the OpenMS proteomic pipeline) ist eine Pipeline für die Analyse von
HPLC/MS-Daten. Sie enthält einen Satz an kleinen Programmen, die verkettet
werden können, um eine Analysen-Pipeline für ein bestimmtes Problem zu
erstellen.
Dieses Paket ist ein Metapaket, das sowohl von OpenMS' Bibliothekspaket
libopenms (libOpenMS und libOpenMS_GUI) als auch vom Paket der
proteomischen Pipeline (topp) abhängt.
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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Versions of package python3-pymzml |
Release | Version | Architectures |
trixie | 2.5.10+repack1-1 | all |
sid | 2.5.10+repack1-1 | all |
bullseye | 2.4.7-3 | all |
stretch | 0.7.6-dfsg-4 | all |
bookworm | 2.5.2+repack1-1 | all |
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License: DFSG free
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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.
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r-cran-maldiquant
GNU R package for quantitative analysis of mass spectrometry data
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Versions of package r-cran-maldiquant |
Release | Version | Architectures |
sid | 1.22.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.22.3-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.22-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.19.3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.18-1 | amd64,arm64,armhf,i386 |
stretch | 1.16.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.11-1 | amd64,armel,armhf,i386 |
Debtags of package r-cran-maldiquant: |
biology | peptidic |
devel | lang:r, library |
field | biology, chemistry, statistics |
role | devel-lib |
science | plotting |
use | analysing |
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License: DFSG free
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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.
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r-cran-maldiquantforeign
GNU R package providing import/export routines for MALDIquant
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Versions of package r-cran-maldiquantforeign |
Release | Version | Architectures |
stretch | 0.10.1-1 | all |
buster | 0.12-1 | all |
bullseye | 0.12-2 | all |
bookworm | 0.13-1 | all |
trixie | 0.14.1-1 | all |
sid | 0.14.1-1 | all |
jessie | 0.9-2 | amd64,armel,armhf,i386 |
Debtags of package r-cran-maldiquantforeign: |
devel | lang:r |
field | biology, chemistry |
use | analysing |
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License: DFSG free
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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.
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r-cran-mixtools
GNU R tools for analyzing finite mixture models
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Versions of package r-cran-mixtools |
Release | Version | Architectures |
sid | 2.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.2-1 | amd64,armel,armhf,i386 |
stretch | 1.0.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.0-2 | amd64,arm64,armhf,i386 |
bullseye | 1.2.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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r-cran-readbrukerflexdata
GNU R package to read Bruker Daltonics *flex format files
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Versions of package r-cran-readbrukerflexdata |
Release | Version | Architectures |
sid | 1.9.3-1 | all |
jessie | 1.8-1 | amd64,armel,armhf,i386 |
stretch | 1.8.3-1 | all |
buster | 1.8.5-2 | all |
bullseye | 1.8.5-3 | all |
bookworm | 1.9.0-1 | all |
trixie | 1.9.3-1 | all |
Debtags of package r-cran-readbrukerflexdata: |
devel | lang:r, library |
field | biology, chemistry, statistics |
role | devel-lib |
use | analysing |
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License: DFSG free
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The readBrukerFlexData package reads data files acquired by MALDI-TOF MS on
Bruker Daltonics machines of the *flex series.
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r-cran-readmzxmldata
GNU R package to read mass spectrometry data in mzXML format
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Versions of package r-cran-readmzxmldata |
Release | Version | Architectures |
jessie | 2.8-1 | amd64,armel,armhf,i386 |
stretch | 2.8.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.8.1-3 | all |
bullseye | 2.8.1-4 | all |
bookworm | 2.8.2-1 | all |
trixie | 2.8.3-1 | all |
sid | 2.8.3-1 | all |
Debtags of package r-cran-readmzxmldata: |
devel | lang:r |
field | biology, chemistry |
use | analysing |
works-with-format | xml |
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License: DFSG free
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The readMzXmlData package contains functions for reading
mass spectrometry data in mzXML format.
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r-other-amsmercury
efficient calculation of accurate masses and abundances of isotopic peaks
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Versions of package r-other-amsmercury |
Release | Version | Architectures |
sid | 1.3.0-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.3.0-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.3.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.3.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.3.0-3 | amd64,arm64,armhf,i386 |
stretch | 1.3.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.3.0-1 | amd64,armel,armhf,i386 |
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License: DFSG free
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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.
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r-other-curvefdp
Schätzung des Konfidenzniveaus für Peptid-Identifikationen
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Versions of package r-other-curvefdp |
Release | Version | Architectures |
bookworm | 2.0-6 | all |
jessie | 2.0-1 | all |
stretch | 2.0-2 | all |
buster | 2.0-5 | all |
bullseye | 2.0-6 | all |
trixie | 2.0-6 | all |
sid | 2.0-6 | all |
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License: DFSG free
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Dies ist ein GNU R-Paket für die Publikation »Estimating the Confidence of
Peptide-Identifications without Decoy Databases« in »Analytical Chemistry«.
Die Funktion curveFDR(scores) passt ein »gaussian mixture model« an eine große
Verteilung von Peptid-Identifikationen an und ermöglicht so die Einschätzung
von Konfidenzniveaus, die auf dem Anteil der Fehlerkennungen beruhen.
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r-other-iwrlars
least angle regression, lasso, positive lasso and forward stagewise
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Versions of package r-other-iwrlars |
Release | Version | Architectures |
stretch | 0.9-5-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.9-5-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.9-5-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.9-5-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.9-5-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.9-5-1 | amd64,armel,armhf,i386 |
buster | 0.9-5-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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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.
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r-other-nitpick
peak identification for mass spectrometry data
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Versions of package r-other-nitpick |
Release | Version | Architectures |
jessie | 2.0-1 | all |
bullseye | 2.0-7 | all |
bookworm | 2.0-7 | all |
trixie | 2.0-7 | all |
sid | 2.0-7 | all |
buster | 2.0-5 | all |
stretch | 2.0-2 | all |
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License: DFSG free
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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.
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tandem-mass
mass spectrometry software for protein identification
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Versions of package tandem-mass |
Release | Version | Architectures |
trixie | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 201702011-1 | amd64,arm64,armhf,i386 |
stretch | 20151215-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 201702011-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2013.09.01-2 | amd64,armel,armhf,i386 |
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License: DFSG free
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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.
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toppic
Top-down proteoform identification and characterization (programs)
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Versions of package toppic |
Release | Version | Architectures |
bookworm | 1.5.3+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.5.3+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.5.3+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.3.0+dfsg1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.7.8 |
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License: DFSG free
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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.
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xtpcpp
C++ version of X!TandemPipeline
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Versions of package xtpcpp |
Release | Version | Architectures |
bullseye | 0.4.18-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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
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Official Debian packages with lower relevance
libisospec++-dev
Isotopic fine structure calculator (C++ development files)
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Versions of package libisospec++-dev |
Release | Version | Architectures |
sid | 2.2.1-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.2.1-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.9.1-5 | amd64,arm64,armhf,i386 |
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License: DFSG free
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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.
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libpwiz-dev
library to perform proteomics data analyses (devel files)
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Versions of package libpwiz-dev |
Release | Version | Architectures |
bullseye | 3.0.18342-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.18342-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.18342-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.0.6585-2 | amd64,armel,armhf,i386 |
stretch | 3.0.9393-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.18342-2 | amd64,arm64,armhf,i386 |
Debtags of package libpwiz-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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libpwizlite-dev
Library to load mzML/mzXML files (dev files)
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Versions of package libpwizlite-dev |
Release | Version | Architectures |
bullseye | 3.0.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.0.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.0.8-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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Packaging has started and developers might try the packaging code in VCS
biceps
error-tolerant peptide identification
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Versions of package biceps |
Release | Version | Architectures |
VCS | 0.0.201401-1 | all |
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License: BSDlike
Debian package not available
Version: 0.0.201401-1
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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.
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