Abstract
BackgroundTop-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation.ResultsIn this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showed that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution.ConclusionsL-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1140) contains supplementary material, which is available to authorized users.
Highlights
Top-down mass spectrometry plays an important role in intact protein identification and characterization
Cell lysate obtained from Salmonella typhimurium (ST) was analyzed with a C4-based high-performance liquid chromatography (HPLC) column coupled with an LTQ-Orbitrap mass spectrometer
The dot-product is a function for computing the similarity between two vectors, which is used in Hardklör [12]
Summary
Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. Spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. In the last two decades, bottom-up mass spectrometry (MS) has been the mainstream of proteomics analysis [1,2,3,4] It is efficient and high-throughput for protein identification and quantification, bottom-up MS has its limitations. A key step in top-down spectral interpretation is to deconvolute a complex top-down mass spectrum to a list of monoisotopic masses
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