DebiChem Project
Summary
Analytical biochemistry
DebiChem - analytisk BioChemistry

Denne metapakke vil installere pakker, som gør, at du kan:

  • indlæse og konvertere datafiler for massespektrometri
  • redigere biopolymersekvenser
  • uddybe komplekse arbejdsforløb for massespektrometri
  • udføre proteindatabasesøgninger med brug af tandem-ms-data
  • visualisere og undersøge massespektrometridata
  • simulere isotop-klynger
  • implementere proteomics-arbejdsforløb.

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

DebiChem Analytical biochemistry packages

Official Debian packages with high relevance

Libmstoolkit-tools
libraries for manipulating mass spectrometry data - tools
Versions of package libmstoolkit-tools
ReleaseVersionArchitectures
buster82-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid82-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye82-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 1 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package libpwiz-tools
ReleaseVersionArchitectures
bullseye3.0.18342-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie3.0.6585-2amd64,armel,armhf,i386
stretch3.0.9393-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster3.0.18342-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.0.18342-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 2 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

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).

Please cite: M.C. Chambers, B. MacLean, R. Burke, D. Amode, D.L. Ruderman, S. Neumann, L. Gatto, B. Fischer, B. Pratt, J. Egertson, K. Hoff, D. Kessner, N. Tasman, N. Shulman, B. Frewen, T.A. Baker, M.-Y. Brusniak, C. Paulse, D. Creasy, L. Flashner, K. Kani, C. Moulding, S.L. Seymour, L.M. Nuwaysir, B. Lefebvre, F. Kuhlmann, J. Roark, P. Rainer, S. Detlev, T. Hemenway, A. Huhmer, J. Langridge, B. Connolly, T. Chadick, K. Holly, J. Eckels, E.W. Deutsch, R.L. Moritz, J.E. Katz, D.B. Agus, M. MacCoss, D.L. Tabb and P. Mallick: A cross-platform toolkit for mass spectrometry and proteomics.. (PubMed) Nature Biotechnology 30:918-920 (2012)
Lutefisk
De novo-fortolkning af peptide CID-spektre
Versions of package lutefisk
ReleaseVersionArchitectures
stretch1.0.7+dfsg-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.0.7+dfsg-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.0.7+dfsg-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.0.7+dfsg-7amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie1.0.7+dfsg-4amd64,armel,armhf,i386
wheezy1.0.5a.cleaned-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze1.0.5a.cleaned-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package lutefisk:
fieldbiology, chemistry
roleprogram
sciencecalculation
Popcon: 1 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

Lutefisk udfører en de novo-fortolkning af kollisionspåførte nedbrydningsspektre (CID), ved at give brugeren en fil indeholdende alle de mulige sekvenskandidater, der svarer til CID-dataene.

Massxpert
Polymer kemimodelopbygning og massespektrometridatasimulering - kørselstid
Versions of package massxpert
ReleaseVersionArchitectures
sid6.0.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie3.4.1-1amd64,armel,armhf,i386
stretch3.6.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze2.3.6-1squeeze1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye6.0.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
wheezy3.2.3-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package massxpert:
biologynuceleic-acids, peptidic
fieldbiology, chemistry
interfacex11
roleprogram
uitoolkitqt
useanalysing, simulating
works-withbiological-sequence
works-with-formatxml
x11application
Popcon: 6 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

MassXpert gør det muligt at udføre de følgende opgaver:

  • Lav helt nye polymer-kemidefinitioner
  • Brug definitionerne til nemt at udføre beregninger lig en skrivebordslommeregninger
  • Udfør sofistikeret sekvensredigering af polymere samt simuleringer
  • Udfør m/z listesammenligninger

Kemiske simuleringer omfatter spaltning (enten kemisk eller enzymatisk), gas-fase-fragmentationer, kemisk ændring af monomer i polymersekvensen, krydsforbinding af monomere i sekvensen, arbitrære massesøgninger.

Denne pakke indeholder programmet massXpert.

Registry entries: Bio.tools  OMICtools 
Minexpert2
MS^n-massespektrometrisk datavisualisering og mining - kørselstid
Versions of package minexpert2
ReleaseVersionArchitectures
bullseye7.4.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid8.1.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 2 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

mineXpert2 gør at brugeren kan udføre de følgende opgaver:

  • Åbne massespektromidatafiler (mzML, mzXML, asc, xy ...)
  • Vise i en tabelvisning det fulde datasæt, for nem filtrering
  • Beregn og vis TIC-chromatogram
  • Beregn og vis et mz=f(rt)-farvekort
  • For mobilitetsdata, beregn og vis et mz=f(dt)-farvekort
  • Integrer massespektrometriske data fra enhver slags datarepræsentation (mass | drift spectra, TIC | XIC chromatogram, 2D-farvekort) til enhver slags datarepræsentation
  • For enhver massedatafunktion (mass peak, TIC | XIC peak, color map) integrer til en en XIC-enkelt intensitetsværdi
  • Funktionsrig isotopisk klyngeberegning startende fra en kemisk formel, valgfrit med brugerdefinerede isotopiske overflodsforhold
  • Gaussisk pasning over enhver isotopisk klynge for at estimere gennemsnitlig masse af en given ion
  • Musedrevet deconvolution af m/z-data (charge envelope-baseret eller isotopisk klyngebaseret)
  • Eksporter dataene til tekstfiler
  • Eksporter den grafiske repræsentation for massespektrometriske data til grafiske filer i et antal formater (jpg, png, pdf)

Denne pakke indeholder programmet mineXpert2.

Registry entries: Bio.tools  OMICtools 
Mmass
Massespektrometriværktøj for proteomik
Versions of package mmass
ReleaseVersionArchitectures
stretch5.5.0-5all
squeeze2.4.0-4all
buster5.5.0-5all
jessie5.5.0-4all
wheezy5.1.0-2all
Debtags of package mmass:
fieldbiology, chemistry
interfacex11
roleprogram
scienceplotting, visualisation
scopeapplication
uitoolkitgtk, wxwidgets
useanalysing
works-withbiological-sequence, db
works-with-formatxml
x11application
Popcon: 9 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

mMass er en fri massespektrum fremviser/analyseprogram hvor de følgende proteomikrelaterede opgaver kan udføres:

  • Åbn rå tekst, mzXML- og mzData-massespektra
  • Definer højdelister
  • Funktionsrig massespektrumsfremviser (zoom, markør ...)
  • Omkalibrering af data
  • Simulationer kun med proteiner
  • Mascot-søgninger på nettet

Programmet kan nemt udvides med yderligere Pythonmoduler. Denne pakke indeholder de platformsuafhængige dele af programmet.

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)
Screenshots of package mmass
Openms
Pakke for LC/MS-datahåndtering og -analyse
Versions of package openms
ReleaseVersionArchitectures
sid2.5.0+cleaned1-5all
jessie1.11.1-5all
bullseye2.6.0+cleaned1-3all
sid2.6.0+cleaned1-3all
buster2.4.0-real-1all
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

OpenMS er en pakke for LC/MS-datahåndtering og -analyse. OpenMS tilbyder en infrastruktur for udvikling af programmer relateret til massespektrometri og funktionsrige 2D- og 3D-virtualiseringsløsninger.

TOPP (OpenMS proteomisk datakanal) er en datakanal for analyse af HPLC/MS-data. Det består af et sæt af utallige små programmer, som kan kædes sammen for at oprette analysedatakanaler skræddersyet for et specifikt problem.

Denne pakke er en metapakke, som afhænger af både bibliotekspakken libopenms (libOpenMS og libOpenMS_GUI) og pakken OpenMS Proteomic Pipeline (topp).

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)
Registry entries: Bio.tools  SciCrunch  OMICtools  Bioconda 
Screenshots of package openms
Python3-pymzml
mzML mass spectrometric data parsing (Python 3.x)
Versions of package python3-pymzml
ReleaseVersionArchitectures
bullseye2.4.7-3all
stretch0.7.6-dfsg-4all
sid2.4.7-3all
Popcon: 4 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

python-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-pakke til kvantitativ analyse af massespektrometri data
Versions of package r-cran-maldiquant
ReleaseVersionArchitectures
jessie1.11-1amd64,armel,armhf,i386
stretch1.16.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.18-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.19.3-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.19.3-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package r-cran-maldiquant:
biologypeptidic
devellang:r, library
fieldbiology, chemistry, statistics
roledevel-lib
scienceplotting
useanalysing
Popcon: 11 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

MALDIquant tilbyder en komplet analyse pipeline for MALDI-TOF og andre massespektrometriske data. Særlige funktioner omfatter baseline subtraktion ved hjælp af SNIP-algoritme, toppunktstilpasning ved hjælp af warp-funktioner, håndtering af replikerede målinger samt ved at tillade spektre med forskellige opløsninger.

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-pakker der tilbyder import/eksport-rutiner for MALDIquant
Versions of package r-cran-maldiquantforeign
ReleaseVersionArchitectures
sid0.12-2all
jessie0.9-2amd64,armel,armhf,i386
stretch0.10.1-1all
buster0.12-1all
bullseye0.12-2all
Debtags of package r-cran-maldiquantforeign:
devellang:r
fieldbiology, chemistry
useanalysing
Popcon: 9 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

MALDIquantForeign-pakken læser (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5) og skriver (tab, csv, msd, mzML) forskellige filformater for massespektrometridata til/fra MALDIquant- objekter.

R-cran-mixtools
GNU R tools for analyzing finite mixture models
Versions of package r-cran-mixtools
ReleaseVersionArchitectures
bullseye1.2.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie1.0.2-1amd64,armel,armhf,i386
stretch1.0.4-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.1.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.2.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 12 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

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-pakke til at læse Bruker dAltonics *flex-formatfiler
Versions of package r-cran-readbrukerflexdata
ReleaseVersionArchitectures
buster1.8.5-2all
sid1.8.5-3all
bullseye1.8.5-3all
stretch1.8.3-1all
jessie1.8-1amd64,armel,armhf,i386
Debtags of package r-cran-readbrukerflexdata:
devellang:r, library
fieldbiology, chemistry, statistics
roledevel-lib
useanalysing
Popcon: 11 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Pakken readBrukerFlexDAta læser datafilerne indhentet af MALDI-TOF MS på Bruker Daltonics-maskiner i *flex-serien.

R-cran-readmzxmldata
GNU R-pakke til at læse massespektrometridata i mzXML-format
Versions of package r-cran-readmzxmldata
ReleaseVersionArchitectures
buster2.8.1-3all
bullseye2.8.1-4all
sid2.8.1-4all
jessie2.8-1amd64,armel,armhf,i386
stretch2.8.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package r-cran-readmzxmldata:
devellang:r
fieldbiology, chemistry
useanalysing
works-with-formatxml
Popcon: 11 users (3 upd.)*
Versions and Archs
License: DFSG free
Git

Pakken readMzXmlData indeholder funktioner for læsning af massespektrometridata i mzXML-formatet.

R-other-amsmercury
Effektiv beregning af nøjagtige masser og mængderne af isotopiske toppe
Versions of package r-other-amsmercury
ReleaseVersionArchitectures
buster1.3.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.3.0-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.3.0-1amd64,armel,armhf,i386
sid1.3.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye1.3.0-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 3 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

Denne GNU R-pakke tilbyder effektiv beregning af nøjagtige masser og mængderne af isotopiske toppe. Det er en forudsætning for R NITPICK, som udfører topidentifikation for massespektrometridata.

R-other-curvefdp
estimation of confidence levels for peptide identifications
Versions of package r-other-curvefdp
ReleaseVersionArchitectures
jessie2.0-1all
stretch2.0-2all
bullseye2.0-6all
sid2.0-6all
buster2.0-5all
Popcon: 3 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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
Mindste vinkelregression, lasso, positiv lasso og fremad stagewise
Versions of package r-other-iwrlars
ReleaseVersionArchitectures
stretch0.9-5-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.9-5-1amd64,armel,armhf,i386
sid0.9-5-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye0.9-5-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster0.9-5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 3 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

Denne GNU R-pakke indeholder effektive procedurer for montering af en hel lassosekvens med prisen på en enkelt mindste kvadraters-tilpasning. Mindste vinkelregression og infinitessimal fremad stagewise-regression er relateret til lasso beskrevet i http://www- stat.stanford.edu/~hastie/Papers/#LARS.

Dette er en modificeret version af den oprindelige pakke lars ved Hastie og Efron, der tilbyder en LARS-modifikation for ikke-negative lasso.

R-other-nitpick
peak identification for mass spectrometry data
Versions of package r-other-nitpick
ReleaseVersionArchitectures
bullseye2.0-7all
sid2.0-7all
stretch2.0-2all
buster2.0-5all
jessie2.0-1all
Popcon: 3 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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
Massespektrometriprogram for proteinidentifikation
Versions of package tandem-mass
ReleaseVersionArchitectures
bullseye201702011-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie2013.09.01-2amd64,armel,armhf,i386
stretch20151215-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster201702011-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid201702011-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 19 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

X! Tandem kan matche tandem-massespektre med peptidsekvenser, i en proces, der er almindeligt anvendt til at udføre proteinidentifikation.

Dette program har en meget enkel og ukompliceret programmeringsgrænseflade: Det tager simpelthen en XML-fil med instruktioner på sin kommandolinje, og viser resultaterne i en XML-fil, der er specificeret i den anvendte XML-fil. Resultatfilens format er beskrevet på http://www.thegpm.org/docs/X_series_output_form.pdf

I modsætning til nogle tidligere søgemaskiner beregner alle X!-seriens søgemaskiner statistisk tillid (forventningsværdier) for alle de individuelle spektrum-til-sekvens opgaver. De samler også alle peptidopgaverne i et datasæt på de kendte proteinsekvenser og tildeler den statistiske tillid at denne samling og justering ikke er tilfældig. Formlen for dette kan findes her. Derfor er der ikke brug for separate samlings- og statistiske analyseprogrammer, f.eks. PeptideProphet og ProteinProphet.

Toppic
Top-down proteoform - identifikation og karakteristik - programmer
Versions of package toppic
ReleaseVersionArchitectures
bullseye1.3.0+dfsg1-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.3.0+dfsg1-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.4.12
Popcon: 1 users (1 upd.)*
Newer upstream!
License: DFSG free
Git

TopPIC Suite består af fire programværktøjer for fortolkningen af top-down massespektrometridata: TopFD, TopPIC, TopMG og TopDiff.

-TopFD (Top-down mass spectral Feature Detection) er et værktøj for

   top-down spektral deconvolution og en efterfølger til MS-Deconv.
 -TopPIC (Top-down mass spectrometry based Proteoform Identification
   and Characterization) identificerer og karakteriserer proteoformer
   på proteome-niveau ved at søge top-down tandem mass spectra mod en
   proteinsekvensdatabasen.
 -TopMG (Top-down mass spectrometry based proteoform identification
   using Mass Graphs) er et værktøj til at identificere ultra-ændrede
   proteoformer ved at søge top-down tandem mass spectra mod en
   proteinsekvensdatabase.
 -TopDiff (Top-down mass spectrometry-based identification of
   Differentially expressed proteoforms) sammenligner overfloden af
   proteoformer og finder differentielt udtrykte proteoformer ved hjælp
   af identifikationer af top-down massespektrometridata for flere
   proteiner.
Xtpcpp
C++-version af X!TandemPipeline
Versions of package xtpcpp
ReleaseVersionArchitectures
bullseye0.4.18-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.4.18-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 4 users (11 upd.)*
Versions and Archs
License: DFSG free

Programmet gør, at du kan udføre de følgende opgaver:

  • Læser X!Tandem xml-resultatfiler
  • Læser MASCOT dat-resultatfiler
  • Læser TPP pepXML-resultatfiler
  • Læser PSI mzIdentML-resultatfiler
  • Run X!Tandem analyserer igennem en grafisk brugerflade
  • Implementerer diverse filtre baseret på statistiske værdier
  • Funktionsrig original algoritme til gruppering til at filtrere redundans
  • Phosphopeptide-tilstand til at håndtere phosphoproteomics-datasæt
  • Rediger, søg og sorter data grafisk
  • XIC chromatogram-browser (eXtracted Ion Current)
  • Sammenligninger af teoretiske isotopmønstre til målte MS1 XIC-områder
  • Eksporter data direkte til Microsoft Office 2010 and LibreOffice (ods eksport)
  • Håndter store datasæt meget hurtigt
  • Udfør peptid kvantificering via MassChroQml-eksport
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)
Versions of package libisospec++-dev
ReleaseVersionArchitectures
sid2.1.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
buster1.9.1-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.1.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 2 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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
Bibliotek til at udføre proteomics-dataanalyser - udviklingsfiler
Versions of package libpwiz-dev
ReleaseVersionArchitectures
jessie3.0.6585-2amd64,armel,armhf,i386
bullseye3.0.18342-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
stretch3.0.9393-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster3.0.18342-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.0.18342-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package libpwiz-dev:
devellibrary
roledevel-lib
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

Biblioteket libpwiz fra projektet ProteoWizard tilbyder et modulopbygget sæt af værktøjer og biblioteker for flere platforme, der kan udvides. Værktøjerne udfører proteomics-dataanalyser; bibliotekerne aktiverer hurtig værktøjsoprettelse ved at tilbyde en robust, klar til tilslutning udviklingsramme, der forenkler og forener datafiladgang, og udfører standardkemi og LCMS-datasætberegninger.

Det primære formål med ProteoWizard er at eliminere de eksisterende barrierer til proteomic-programudvikling, så at forskere kan fokusere på udvikling af nye analytiske fremgangsmåder, frem for at skulle dedikere signifikante ressourcer til hverdagsagtige (hvis vigtige) opgaver, såsom at læse datafiler.

Denne pakke indeholder udviklingsfilerne for biblioteket.

Please cite: M.C. Chambers, B. MacLean, R. Burke, D. Amode, D.L. Ruderman, S. Neumann, L. Gatto, B. Fischer, B. Pratt, J. Egertson, K. Hoff, D. Kessner, N. Tasman, N. Shulman, B. Frewen, T.A. Baker, M.-Y. Brusniak, C. Paulse, D. Creasy, L. Flashner, K. Kani, C. Moulding, S.L. Seymour, L.M. Nuwaysir, B. Lefebvre, F. Kuhlmann, J. Roark, P. Rainer, S. Detlev, T. Hemenway, A. Huhmer, J. Langridge, B. Connolly, T. Chadick, K. Holly, J. Eckels, E.W. Deutsch, R.L. Moritz, J.E. Katz, D.B. Agus, M. MacCoss, D.L. Tabb and P. Mallick: A cross-platform toolkit for mass spectrometry and proteomics.. (PubMed) Nature Biotechnology 30:918-920 (2012)
Libpwizlite-dev
Library to load mzML/mzXML files (dev files)
Versions of package libpwizlite-dev
ReleaseVersionArchitectures
sid3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0.3-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Popcon: 0 users (1 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package biceps
ReleaseVersionArchitectures
VCS0.0.201401-1all
Versions and Archs
License: BSDlike
Debian package not available
Git
Version: 0.0.201401-1

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)
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203033