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A new scoring function for top-down spectral deconvolution.

Kou Q, Wu S, Liu X - BMC Genomics (2014)

Bottom Line: 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.L-score shows high discriminative ability in identification of isotopomer envelopes.

View Article: PubMed Central - PubMed

Affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 535 W, Michigan Street, Indianapolis, IN 46202, USA. xwliu@iupui.edu.

ABSTRACT

Background: 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. 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.

Results: In 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.

Conclusions: L-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.

No MeSH data available.


Comparison of Decon2LS, MS-Deconv, and MS-Deconv+ on spectral identification by coupling them with MS-Align+. The numbers of tandem mass spectra identified from the EC HCD and ETD data sets by the three methods with 1% protein level FDR are compared. (a) The EC HCD data set. (b) The EC ETD data set.
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Fig6: Comparison of Decon2LS, MS-Deconv, and MS-Deconv+ on spectral identification by coupling them with MS-Align+. The numbers of tandem mass spectra identified from the EC HCD and ETD data sets by the three methods with 1% protein level FDR are compared. (a) The EC HCD data set. (b) The EC ETD data set.

Mentions: All the tandem mass spectra in the EC HCD and ETD data sets were deconvoluted by Decon2LS, MS-Deconv, and MS-Deconv+; the deconvoluted mass lists reported by the three tools were searched against the EC proteome for protein identification using MS-Align+ [15]. (See Additional file 1 for the parameter settings of MS-Align+ and the three tools.) The EC proteome database was downloaded from the Swiss-Prot database, and a shuffled database of the same size was concatenated to the target protein database for estimation of FDRs. With 1% protein level FDR, MS-Deconv+ coupled with MS-Align+ identified more spectra (1,585 in HCD and 1,223 in ETD) than MS-Deconv (1,543 in HCD and 1,216 in ETD) and Decon2LS (1,526 in HCD and 620 in ETD) (Figure 6). The three methods shared a total of 1,352 spectral identifications in the EC HCD data set and 607 spectral identifications in the EC ETD data set. Although the performances of MS-Deconv+ and MS-Deconv were similar in the number of identified spectra, MS-Deconv+ reported more matched monoisotopic masses (55,731 in HCD and 24,235 in ETD) than MS-Deconv (41079 in HCD and 21,360 in ETD) and Decon2LS (39,991 in HCD and 10,479 in ETD) for the spectra identified by all the tools. These matched masses play an important role in localizing various changes in identified proteoforms.Figure 6


A new scoring function for top-down spectral deconvolution.

Kou Q, Wu S, Liu X - BMC Genomics (2014)

Comparison of Decon2LS, MS-Deconv, and MS-Deconv+ on spectral identification by coupling them with MS-Align+. The numbers of tandem mass spectra identified from the EC HCD and ETD data sets by the three methods with 1% protein level FDR are compared. (a) The EC HCD data set. (b) The EC ETD data set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4378558&req=5

Fig6: Comparison of Decon2LS, MS-Deconv, and MS-Deconv+ on spectral identification by coupling them with MS-Align+. The numbers of tandem mass spectra identified from the EC HCD and ETD data sets by the three methods with 1% protein level FDR are compared. (a) The EC HCD data set. (b) The EC ETD data set.
Mentions: All the tandem mass spectra in the EC HCD and ETD data sets were deconvoluted by Decon2LS, MS-Deconv, and MS-Deconv+; the deconvoluted mass lists reported by the three tools were searched against the EC proteome for protein identification using MS-Align+ [15]. (See Additional file 1 for the parameter settings of MS-Align+ and the three tools.) The EC proteome database was downloaded from the Swiss-Prot database, and a shuffled database of the same size was concatenated to the target protein database for estimation of FDRs. With 1% protein level FDR, MS-Deconv+ coupled with MS-Align+ identified more spectra (1,585 in HCD and 1,223 in ETD) than MS-Deconv (1,543 in HCD and 1,216 in ETD) and Decon2LS (1,526 in HCD and 620 in ETD) (Figure 6). The three methods shared a total of 1,352 spectral identifications in the EC HCD data set and 607 spectral identifications in the EC ETD data set. Although the performances of MS-Deconv+ and MS-Deconv were similar in the number of identified spectra, MS-Deconv+ reported more matched monoisotopic masses (55,731 in HCD and 24,235 in ETD) than MS-Deconv (41079 in HCD and 21,360 in ETD) and Decon2LS (39,991 in HCD and 10,479 in ETD) for the spectra identified by all the tools. These matched masses play an important role in localizing various changes in identified proteoforms.Figure 6

Bottom Line: 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.L-score shows high discriminative ability in identification of isotopomer envelopes.

View Article: PubMed Central - PubMed

Affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 535 W, Michigan Street, Indianapolis, IN 46202, USA. xwliu@iupui.edu.

ABSTRACT

Background: 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. 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.

Results: In 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.

Conclusions: L-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.

No MeSH data available.