Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)
| Autor: | David Clarke, Sean Peters, Akila J. Seneviratne, Michael Hecker, Brett Tully, Michael Dausmann, Qing Zhong, Peter G. Hains |
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| Rok vydání: | 2020 |
| Předmět: |
Statistics and Probability
AcademicSubjects/SCI01060 Computer science Noise reduction Gene Expression Mass spectrometry Proteomics Biochemistry 2D undecimated wavelet transform Software Liquid chromatography–mass spectrometry Molecular Biology business.industry Wavelet transform Pattern recognition Original Papers proteomics data Computer Science Applications Computational Mathematics Noise Identification (information) Computational Theory and Mathematics Artificial intelligence business peptide identification |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 |
| Popis: | Motivation The output of electrospray ionization–liquid chromatography mass spectrometry (ESI-LC-MS) is influenced by multiple sources of noise and major contributors can be broadly categorized as baseline, random and chemical noise. Noise has a negative impact on the identification and quantification of peptides, which influences the reliability and reproducibility of MS-based proteomics data. Most attempts at denoising have been made on either spectra or chromatograms independently, thus, important 2D information is lost because the mass-to-charge ratio and retention time dimensions are not considered jointly. Results This article presents a novel technique for denoising raw ESI-LC-MS data via 2D undecimated wavelet transform, which is applied to proteomics data acquired by data-independent acquisition MS (DIA-MS). We demonstrate that denoising DIA-MS data results in the improvement of peptide identification and quantification in complex biological samples. Availability and implementation The software is available on Github (https://github.com/CMRI-ProCan/CRANE). The datasets were obtained from ProteomeXchange (Identifiers—PXD002952 and PXD008651). Preliminary data and intermediate files are available via ProteomeXchange (Identifiers—PXD020529 and PXD025103). Supplementary information Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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