Hi Cansu,

a very nice package that has been developed by people in Mikahil Gorshkov's group in Moscow is pyteomics (it can do a lot more than RT prediction):

http://pythonhosted.org//pyteomics/

Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013) “Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics”, Journal of The American Society for Mass Spectrometry, 24(2), 301–304. DOI: 10.1007/s13361-012-0516-6

Best wishes,

Achim

Hi Cansu,

a very nice package that has been developed by people in Mikahil Gorshkov's group in Moscow is pyteomics (it can do a lot more than RT prediction):

http://pythonhosted.org//pyteomics/

Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013) “Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics”, Journal of The American Society for Mass Spectrometry, 24(2), 301–304. DOI: 10.1007/s13361-012-0516-6

Best wishes,

Achim

You might also want to look at Skyline which implements iRT for retention time prediction. Skyline is excellent free software with great support and tutorials available online. Which way you go will depend on your workflow. Despite first appearances, Skyline is not just for SRM data.

Software;

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

MacLean, B. et al. Skyline: an open source document editor for creating and analysing targeted proteomics experiments. Bioinformatics 26, 966 –968 (2010).

iRT tutorial

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_irt

Escher, C. et al. Using iRT, a normalised retention time for more targeted measurement of peptides. Proteomics 12, 1111–1121 (2012).

Another popular one would be SSRCalc;

Krokhin, O. V. Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal. Chem. 78, 7785–7795 (2006).

This is also implemented in Skyline and is bound to be in other software out there.

A quick search pulled out this website;

http://hs2.proteome.ca/SSRCalc/SSRCalcX.html

Hope that helps,

Peter

Hi,

there's also a web-interface to a BioLCCC algorithm, which Achim Treumann have already mentioned as implemented in Pyteomics package:

http://theorchromo.ru/