Question: Open Source Mass Spec Search Engines?
6
gravatar for Jdnavarro
9.9 years ago by
Jdnavarro410
Sevilla, Spain
Jdnavarro410 wrote:

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 • 3.8k views
ADD COMMENTlink written 9.9 years ago by Jdnavarro410

sorry, is what you are asking related to Peptide Mass Fingerprinting? Or is it a different technique? thanks

ADD REPLYlink written 9.9 years ago by Giovanni M Dall'Olio27k

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

ADD REPLYlink written 9.9 years ago by Jdnavarro410
3
gravatar for Dawe
9.9 years ago by
Dawe270
Milan
Dawe270 wrote:

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

ADD COMMENTlink written 9.9 years ago by Dawe270

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

ADD REPLYlink written 9.0 years ago by Craig30
3
gravatar for Mrawlins
9.9 years ago by
Mrawlins420
Retirement
Mrawlins420 wrote:

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.

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.9 years ago by Mrawlins420

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

ADD REPLYlink written 9.9 years ago by Jdnavarro410
3
gravatar for Michael Dondrup
9.9 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

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....

ADD COMMENTlink written 9.9 years ago by Michael Dondrup47k
2
gravatar for Brianbalgley
9.9 years ago by
Brianbalgley100
Brianbalgley100 wrote:

try: http://human.thegpm.org/tandem/thegpm_tandem.html and http://h201.thegpm.org/tandem/thegpm_hunter.html

ADD COMMENTlink written 9.9 years ago by Brianbalgley100
1
gravatar for Julian
9.9 years ago by
Julian200
Manchester, UK
Julian200 wrote:

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.

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.9 years ago by Julian200

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

ADD REPLYlink written 5 months ago by xiaoguang30
0
gravatar for Darked89
9.9 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

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

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.9 years ago by Darked894.2k
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