+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model

A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model

Bmc Genomics 16(Suppl. 12): S12

Mass Spectrometry (MS) is a ubiquitous analytical tool in biological research and is used to measure the mass-to-charge ratio of bio-molecules. Peak detection is the essential first step in MS data analysis. Precise estimation of peak parameters such as peak summit location and peak area are critical to identify underlying bio-molecules and to estimate their abundances accurately. We propose a new method to detect and quantify peaks in mass spectra. It uses dual-tree complex wavelet transformation along with Stein's unbiased risk estimator for spectra smoothing. Then, a new method, based on the modified Asymmetric Pseudo-Voigt (mAPV) model and hierarchical particle swarm optimization, is used for peak parameter estimation. Using simulated data, we demonstrated the benefit of using the mAPV model over Gaussian, Lorentz and Bi-Gaussian functions for MS peak modelling. The proposed mAPV model achieved the best fitting accuracy for asymmetric peaks, with lower percentage errors in peak summit location estimation, which were 0.17% to 4.46% less than that of the other models. It also outperformed the other models in peak area estimation, delivering lower percentage errors, which were about 0.7% less than its closest competitor - the Bi-Gaussian model. In addition, using data generated from a MALDI-TOF computer model, we showed that the proposed overall algorithm outperformed the existing methods mainly in terms of sensitivity. It achieved a sensitivity of 85%, compared to 77% and 71% of the two benchmark algorithms, continuous wavelet transformation based method and Cromwell respectively. The proposed algorithm is particularly useful for peak detection and parameter estimation in MS data with overlapping peak distributions and asymmetric peaks. The algorithm is implemented using MATLAB and the source code is freely available at http://mapv.sourceforge.net.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 057076026

Download citation: RISBibTeXText

PMID: 26680279

DOI: 10.1186/1471-2164-16-s12-s12

Related references

Ion trace detection algorithm to extract pure ion chromatograms to improve untargeted peak detection quality for liquid chromatography/time-of-flight mass spectrometry-based metabolomics data. Analytical Chemistry 87(5): 3048-3055, 2015

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. Bmc Bioinformatics 10: 4, 2009

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry. Mass Spectrometry 3(1): A0030, 2014

Nanoparticle-based detection of oxidized phospholipids by MALDI mass spectrometry: nano-MALDI approach. Analytical Chemistry 86(13): 6401-6409, 2014

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information. Journal of Proteome Research 12(1): 328-335, 2013

Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data. Analytical Chemistry 88(21): 10395-10403, 2016

Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data. Ieee/Acm Transactions on Computational Biology and Bioinformatics 8(4): 1054-1066, 2011

Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry. Journal of the American Society for Mass Spectrometry 28(2): 253-262, 2017

Validation of a modified algorithm for the identification of yeast isolates using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). European Journal of Clinical Microbiology and Infectious Diseases 31(5): 841-848, 2012

Surface modified silver selinide nanoparticles as extracting probes to improve peptide/protein detection via nanoparticles-based liquid phase microextraction coupled with MALDI mass spectrometry. Talanta 83(2): 527-534, 2010

Detection of peptides covalently modified with multiple fatty acids by MALDI-TOF mass spectrometry. Journal of Peptide Research 66(2): 94, 2005

A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry. Bmc Bioinformatics 15: 376, 2014

Novel algorithm for simultaneous component detection and pseudo-molecular ion characterization in liquid chromatography-mass spectrometry. Analytica Chimica Acta 853: 402-414, 2015

Analysis of MALDI-TOF mass spectrometry data for detection of glycan biomarkers. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008: 216-227, 2008

Self-assembled-monolayer-modified silicon substrate to enhance the sensitivity of peptide detection for AP-MALDI mass spectrometry. Journal of Mass Spectrometry 42(12): 1628-1636, 2007