EagleEye removes background MS/MS spectra by comparing them with a non-annotated collection of spectra, obtained from combined LC-MS/MS runs of control in-gel digests as well as identified in on-going proteomis projects.
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Junqueira, M., Spirin, V., Balbuena, T. S., Waridel, P., Surendranath, V., Kryukov, G., Adzhubei, I., Thomas, H., Sunyaev, S. and Shevchenko, A.
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.
J Proteome Res. 2008 Aug;7(8):3382-95. Epub 2008 Jun 18.