ArticleAnalytical chemistry2008
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.
Article in Analytical chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Mass Spectrometry for Proteomics-Based Investigation.Advances in experimental medicine and biology · 2026Review
- LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers.Analytical chemistry · 2023Article
- Improved analysis of derivatized steroid hormone isomers using ion mobility-mass spectrometry (IM-MS).Analytical and bioanalytical chemistry · 2023Article
- TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.Journal of proteome research · 2023Article
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles.Experimental & molecular medicine · 2018Article
- A protein profile of visceral adipose tissues linked to early pathogenesis of type 2 diabetes mellitus.Molecular & cellular proteomics : MCP · 2014Article
- Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data.Molecular & cellular proteomics : MCP · 2014Article
- Protein analysis by shotgun/bottom-up proteomics.Chemical reviews · 2013Review
- 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
- Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses.Journal of proteome research · 2012Article
- Normalization and missing value imputation for label-free LC-MS analysis.BMC bioinformatics · 2012Article
- UNiquant, a program for quantitative proteomics analysis using stable isotope labeling.Journal of proteome research · 2011Article
- Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry.Molecular & cellular proteomics : MCP · 2011Article
- Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.Analytical chemistry · 2010Article
- DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.Molecular & cellular proteomics : MCP · 2010Article
- Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry.Methods (San Diego, Calif.) · 2010Article
- Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects.The annals of applied statistics · 2010Article
- Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.Bioinformatics (Oxford, England) · 2009Article
- Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments.Analytical chemistry · 2008Article
Corrections and comments
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14 authors.
Funding
Abstract
The high mass measurement accuracy and precision available with recently developed mass spectrometers is increasingly used in proteomics analyses to confidently identify tryptic peptides from complex mixtures of proteins, as well as post-translational modifications and peptides from nonannotated proteins. To take full advantage of high mass measurement accuracy instruments, it is necessary to limit systematic mass measurement errors. It is well known that errors in m/z measurements can be affected by experimental parameters that include, for example, outdated calibration coefficients, ion intensity, and temperature changes during the measurement. Traditionally, these variations have been corrected through the use of internal calibrants (well-characterized standards introduced with the sample being analyzed). In this paper, we describe an alternative approach where the calibration is provided through the use of a priori knowledge of the sample being analyzed. Such an approach has previously been demonstrated based on the dependence of systematic error on m/z alone. To incorporate additional explanatory variables, we employed multidimensional, nonparametric regression models, which were evaluated using several commercially available instruments. The applied approach is shown to remove any noticeable biases from the overall mass measurement errors and decreases the overall standard deviation of the mass measurement error distribution by 1.2-2-fold, depending on instrument type. Subsequent reduction of the random errors based on multiple measurements over consecutive spectra further improves accuracy and results in an overall decrease of the standard deviation by 1.8-3.7-fold. This new procedure will decrease the false discovery rates for peptide identifications using high-accuracy mass measurements.
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