Open Source Mass Spec Search Engines?
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11.9 years ago
Jdnavarro ▴ 410

I'm looking for open source software to map proteomics spectra to peptides using known protein databases.

Can you point me to the open source mass spec search engines you know? Preferably with simple and readable code.

proteomics • 4.8k views
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sorry, is what you are asking related to Peptide Mass Fingerprinting? Or is it a different technique? thanks

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Sorry, I was referring to peptide fragmentation by tandem mass spec. MS/MS spectra. http://en.wikipedia.org/wiki/Tandem_mass_spectrometry.

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11.9 years ago
Dawe ▴ 270

OMSSA http://pubchem.ncbi.nlm.nih.gov/omssa/

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OMSSA is a great search algorithm, but not exactly the most readable. It is C++ and uses a lot of NCBI components.

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11.9 years ago
Mrawlins ▴ 430

We developed Polygraph. It's based on the algorithm from http://pubs.acs.org/doi/abs/10.1021/jp905049d, which documents some of the preliminary results using a hybrid database/library search. A manuscript with updated results was just submitted for publication, and hopefully will be out the beginning of next year.

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Nice, didn't know about that one. Looking forward for the code release.

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11.9 years ago

Just to add to completeness there is EMOWSE:

http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/emowse.html

It's been there for quite a couple of years now, but at least it's true open-source....

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11.9 years ago
Julian ▴ 200

As well as what has been mentioned above, there are numerous other tools out there - all with slightly different approaches/algorithms (including spectral library approaches). You might want to take a look at http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList which contains a list of proteomics related software including protein identification software.

I presume you are aware that you can access Mascot in a cut down version from http://www.matrixscience.com/ website - I know it is limited and you do put your data "out there", but it is one of the ones that is accepted by journals, etc (albeit with some verification required now).

Personally of the free stuff that I can download and put on my computer, I use X!Tandem and OMSSA, the later of which I have found to be a little more easy to use although not by much. Running combinations of the free search software is usually beneficial too.

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Is there any tutorial for X! Tandem software, I have n’t found it for a long time

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11.9 years ago
Darked89 4.2k

This page is bit dated, but lists few other programs.

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