An operator-independent approach to mass spectral peak identification and integration - PubMed (original) (raw)
. 2004 May 1;76(9):2446-52.
doi: 10.1021/ac0354701.
Affiliations
- PMID: 15117182
- DOI: 10.1021/ac0354701
An operator-independent approach to mass spectral peak identification and integration
William E Wallace et al. Anal Chem. 2004.
Abstract
A mathematical algorithm is presented that locates and calculates the area beneath peaks from real data using only reproducible mathematical operations and no user-selected parameters. It makes no assumptions about peak shape and requires no smoothing or preprocessing of the data. In fact, it is shown that for matrix-assisted laser desorption time-of-flight mass spectra noise exists at all frequency ranges making the smoothing of data without distortion of peak areas impossible. The algorithm is based on a time-series segmentation routine that reduces the data set to groups of three strategic points where each group defines the beginning, center, and ending of each peak located. The peak areas are found from the strategic points using a commonplace polygonal area calculation routine. Peaks with statistically insignificant height or area are then discarded. The performance of the algorithm is demonstrated on a polystyrene mass spectrum with varying degrees of noise added either mathematically or experimentally. An on-line implementation of the method, termed MassSpectator, for public use can be found at www.nist.gov/maldi.
Similar articles
- Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.
Du P, Kibbe WA, Lin SM. Du P, et al. Bioinformatics. 2006 Sep 1;22(17):2059-65. doi: 10.1093/bioinformatics/btl355. Epub 2006 Jul 4. Bioinformatics. 2006. PMID: 16820428 - Improving automatic peptide mass fingerprint protein identification by combining many peak sets.
Rögnvaldsson T, Häkkinen J, Lindberg C, Marko-Varga G, Potthast F, Samuelsson J. Rögnvaldsson T, et al. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Aug 5;807(2):209-15. doi: 10.1016/j.jchromb.2004.04.010. J Chromatogr B Analyt Technol Biomed Life Sci. 2004. PMID: 15203031 - Peak selection from MALDI-TOF mass spectra using ant colony optimization.
Ressom HW, Varghese RS, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, Goldman R. Ressom HW, et al. Bioinformatics. 2007 Mar 1;23(5):619-26. doi: 10.1093/bioinformatics/btl678. Epub 2007 Jan 19. Bioinformatics. 2007. PMID: 17237065 - Improved method for peak picking in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Kempka M, Sjödahl J, Björk A, Roeraade J. Kempka M, et al. Rapid Commun Mass Spectrom. 2004;18(11):1208-12. doi: 10.1002/rcm.1467. Rapid Commun Mass Spectrom. 2004. PMID: 15164350
Cited by
- Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra.
Tabb DL, Shah MB, Strader MB, Connelly HM, Hettich RL, Hurst GB. Tabb DL, et al. J Am Soc Mass Spectrom. 2006 Jul;17(7):903-915. doi: 10.1016/j.jasms.2006.02.003. Epub 2006 May 19. J Am Soc Mass Spectrom. 2006. PMID: 16713712 - Projections Onto Order Simplexes and Isotonic Regression.
Kearsley AJ. Kearsley AJ. J Res Natl Inst Stand Technol. 2006 Apr 1;111(2):121-5. doi: 10.6028/jres.111.011. Print 2006 Mar-Apr. J Res Natl Inst Stand Technol. 2006. PMID: 27274923 Free PMC article. - NITPICK: peak identification for mass spectrometry data.
Renard BY, Kirchner M, Steen H, Steen JA, Hamprecht FA. Renard BY, et al. BMC Bioinformatics. 2008 Aug 28;9:355. doi: 10.1186/1471-2105-9-355. BMC Bioinformatics. 2008. PMID: 18755032 Free PMC article. - Reproducibility in cytometry: Signals analysis and its connection to uncertainty quantification.
Patrone PN, DiSalvo M, Kearsley AJ, McFadden GB, Cooksey GA. Patrone PN, et al. PLoS One. 2023 Dec 22;18(12):e0295502. doi: 10.1371/journal.pone.0295502. eCollection 2023. PLoS One. 2023. PMID: 38134031 Free PMC article. - MathDAMP: a package for differential analysis of metabolite profiles.
Baran R, Kochi H, Saito N, Suematsu M, Soga T, Nishioka T, Robert M, Tomita M. Baran R, et al. BMC Bioinformatics. 2006 Dec 13;7:530. doi: 10.1186/1471-2105-7-530. BMC Bioinformatics. 2006. PMID: 17166258 Free PMC article.
LinkOut - more resources
Full Text Sources