ArticleProteome science2006
Analytical model of peptide mass cluster centres with applications.
Article in Proteome science, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space.Journal of proteome research · 2023Article
- Detecting Modifications in Proteomics Experiments with Param-Medic.Journal of proteome research · 2019Article
- Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.Journal of proteome research · 2017Article
- Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view.BMC bioinformatics · 2014Article
- De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.Journal of the American Society for Mass Spectrometry · 2012Article
- Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.BMC bioinformatics · 2012Article
- Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry.IEEE transactions on signal processing : a publication of the IEEE Signal Processing Society · 2010Article
- Improving mass defect filters for human proteins.Journal of proteome research · 2010Article
- Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments.Bioinformatics (Oxford, England) · 2010Article
- A mass spectrometry primer for mass spectrometry imaging.Methods in molecular biology (Clifton, N.J.) · 2010Article
- Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.BMC research notes · 2008Article
- Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content.Analytical chemistry · 2008Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate peptide mass lists, to identify and remove non-peptide peaks and for data reduction.
resultsWe developed an analytical model of the peptide mass cluster centres. Inputs to the model included, the amino acid frequencies in the sequence database, the average length of the proteins in the database, the cleavage specificity of the proteolytic enzyme used and the cleavage probability. We examined the accuracy of our model by comparing it with the model based on an in silico sequence database digest. To identify the crucial parameters we analysed how the cluster centre location depends on the inputs. The distance to the nearest cluster was used to calibrate mass spectrometric peptide peak-lists and to identify non-peptide peaks.
conclusionThe model introduced here enables us to predict the location of the peptide mass cluster centres. It explains how the location of the cluster centres depends on the input parameters. Fast and efficient calibration and filtering of non-peptide peaks is achieved by a distance measure suggested by Wool and Smilansky.
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Registered trials
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