Difference between revisions of "Other software for Proteomics"

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(Software for protein inference)
 
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== Software for quantitation ==
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== MRM/SRM (Multiple Reaction Monitoring/Selected Reaction Monitoring) ==
 
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# MsQuant
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# MaxQuant
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# [http://fields.scripps.edu/census/index.php Census]
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== MRM/SRM ==
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#[http://proteomics.fhcrc.org/CPL/MRMer.html MRMer]
 
#[http://proteomics.fhcrc.org/CPL/MRMer.html MRMer]
 
#[http://www.mrmaid.info/ MRMaid]
 
#[http://www.mrmaid.info/ MRMaid]
 
#[https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view Skyline]
 
#[https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view Skyline]
#[http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba MaRiMba] Part of TPP
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#[http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba MaRiMba] Part of TPP (Trans-Proteomic Pipeline)
  
== PTMs ==
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== PTMs (Post-Translational Modifications) ==
  
 
# Ascore
 
# Ascore
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# OpenSea (Blind search)
 
# OpenSea (Blind search)
 
# [http://prix.uos.ac.kr/modi/ ModMap] (Blind search)
 
# [http://prix.uos.ac.kr/modi/ ModMap] (Blind search)
 
== Software for protein inference ==
 
 
# ProteinProphet
 
# [http://fenchurch.mc.vanderbilt.edu/bumbershoot/idpicker/index.html IDPicker]
 
# [http://www.parc.com/work/focus-area/mass-spectra-analysis/ Combyne]
 
# [http://bioinf.itmat.upenn.edu/ebp/ EBP]
 
  
 
== Other software ==
 
== Other software ==
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# [http://www.ebi.ac.uk/pride/dod/pages/dodStart.jsf?sessionControlDisabled=true Database on Demand]. Web tool to generate custom FASTA files for peptide identification.
 
# [http://www.ebi.ac.uk/pride/dod/pages/dodStart.jsf?sessionControlDisabled=true Database on Demand]. Web tool to generate custom FASTA files for peptide identification.
  
== Links ==
 
 
* http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList
 
* http://proteome.nih.gov/links.html
 
* http://tools.proteomecenter.org/wiki/index.php?title=Software:Overview
 
* [http://proteowizard.sourceforge.net/technical/tools/index.html ProteoWizard Tools]
 
  
 
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See also the [[Proteomics|portal page]] for the Proteomics task force.
 
See also the [[Proteomics|portal page]] for the Proteomics task force.
  
[[Category:Proteomics:Software]]
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[[Category:Proteomics / Tools]]

Latest revision as of 13:58, 11 April 2011

MRM/SRM (Multiple Reaction Monitoring/Selected Reaction Monitoring)

  1. MRMer
  2. MRMaid
  3. Skyline
  4. MaRiMba Part of TPP (Trans-Proteomic Pipeline)

PTMs (Post-Translational Modifications)

  1. Ascore
  2. Slomo
  3. MS-Alignment (Blind search)
  4. PhosCalc
  5. Modificomb (Blind search)
  6. OpenSea (Blind search)
  7. ModMap (Blind search)

Other software

  1. MassSpecWavelet
  2. mMass
  3. Database on Demand. Web tool to generate custom FASTA files for peptide identification.



See also the portal page for the Proteomics task force.