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Tandem mass spectrometry data quality assessment by self-convolution.

Choo KW, Tham WM - BMC Bioinformatics (2007)

Bottom Line: The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result.The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores.By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Group, Nanyang Polytechnic, 569830 Singapore, Republic Of Singapore. choo_keng_wah@nyp.edu.sg

ABSTRACT

Background: Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on de novo sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified.

Results: The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores.

Conclusion: We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well and could potentially be used as a pre-processing for all mass spectrometry based protein identification tools.

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DC-shifted self-convolution plot of experimental tandem MS. This figure shows the difference between the DC-shifted self-convolution results obtained from the original mass spectrum (left) and the pre-processed mass spectrum (right).
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Figure 6: DC-shifted self-convolution plot of experimental tandem MS. This figure shows the difference between the DC-shifted self-convolution results obtained from the original mass spectrum (left) and the pre-processed mass spectrum (right).

Mentions: The proposed method was subsequently tested on 60 sets of real tandem MS spectra (unpublished). They were subjected to the QS scoring function described in the Eq. 1. We considered 15 highest intensity peaks to the left and right of the mid-point window of each spectrum. The self-convolution result is shown in Fig. 5. The DC shifted self-convolution plots of the original tandem MS spectrum is contrasted with that of the newly generated plot, as shown in Fig. 6. We have also assumed that 30 peaks are sufficient in our calculation, but this number can be increased in the case where more ion fragments are expected. All tandem mass spectra having high scores have been identified successfully using MASCOT [8] with high confidence (> 45).


Tandem mass spectrometry data quality assessment by self-convolution.

Choo KW, Tham WM - BMC Bioinformatics (2007)

DC-shifted self-convolution plot of experimental tandem MS. This figure shows the difference between the DC-shifted self-convolution results obtained from the original mass spectrum (left) and the pre-processed mass spectrum (right).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2164967&req=5

Figure 6: DC-shifted self-convolution plot of experimental tandem MS. This figure shows the difference between the DC-shifted self-convolution results obtained from the original mass spectrum (left) and the pre-processed mass spectrum (right).
Mentions: The proposed method was subsequently tested on 60 sets of real tandem MS spectra (unpublished). They were subjected to the QS scoring function described in the Eq. 1. We considered 15 highest intensity peaks to the left and right of the mid-point window of each spectrum. The self-convolution result is shown in Fig. 5. The DC shifted self-convolution plots of the original tandem MS spectrum is contrasted with that of the newly generated plot, as shown in Fig. 6. We have also assumed that 30 peaks are sufficient in our calculation, but this number can be increased in the case where more ion fragments are expected. All tandem mass spectra having high scores have been identified successfully using MASCOT [8] with high confidence (> 45).

Bottom Line: The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result.The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores.By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Group, Nanyang Polytechnic, 569830 Singapore, Republic Of Singapore. choo_keng_wah@nyp.edu.sg

ABSTRACT

Background: Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on de novo sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified.

Results: The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores.

Conclusion: We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well and could potentially be used as a pre-processing for all mass spectrometry based protein identification tools.

Show MeSH