X!Tandem is a protein search engine available from The Global Proteome Machine Organization that is fast and free. X!Tandem is open source software that automatically searches for missed cleavages, semi-tryptic peptides, post-translational modifications, and point mutations.
X!Tandem was created by Craig and Beavis1,2 of the Manitoba Proteomics Center as an open-source alternative to SEQUEST, Mascot and similar search engines.
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X!Tandem Explained
Like other search engines, X!Tandem matches each tandem spectrum against model spectra created from each peptide in the protein database.
But X!Tandem has its own approach that gives it unique strengths and weaknesses. For a discussion of X!Tandem's approach, its strengths, and a comparison with SEQUEST, continue to the slide presentation "X!Tandem Explained ".
X!Tandem comes packaged with Proteome Software's Scaffold program. Scaffold improves the number and confidence of protein identifications by combining X!Tandem's results with the results of either SEQUEST or Mascot.
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X!Tandem Explained
by Brian Searle
pdf format (115 KB)
Power Point format
18 slides
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References
- Craig, R., and Beavis, R. C.,
"TANDEM: matching proteins with tandem mass spectra."
Bioinformatics. 2004 Jun 12;20(9):1466-7. Epub 2004 Feb 19.
PubMed
- Craig, R., and Beavis, R. C.,
"A method for reducing the time required to match protein sequences with tandem mass spectra."
Rapid Commun. Mass Spectrom. 2003;17(20):2310-6.
PubMed
- Fenyo, D., and Beavis, R. C.,
"A method for assessing the statistical significance of mass spectrometry-based protein
identifications using general scoring schemes."
Anal. Chem. 2003 Feb 15;75(4):768-74.
PubMed
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