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De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

ABSTRACT: We report an algorithm designed for the calibration of low resolution peptide mass spectra. Our algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1 min, with no input required besides the mass spectra themselves. The mass measurement accuracy for a set of spectra collected on an LTQ-Velos improved 20-fold from -0.1776?±?0.0010?m/z to 0.0078?±?0.0006?m/z after calibration (avg?±?95 % confidence interval). The precision in mass measurement was improved due to the correction of non-linear variation in mass measurement accuracy across the m/z range.

SUBMITTER: Egertson JD

PROVIDER: S-EPMC3515694 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

Egertson Jarrett D JD Eng Jimmy K JK Bereman Michael S MS Hsieh Edward J EJ Merrihew Gennifer E GE MacCoss Michael J MJ

Journal of the American Society for Mass Spectrometry 20120925 12

We report an algorithm designed for the calibration of low resolution peptide mass spectra. Our algorithm is implemented in a program called FineTune, which corrects systematic mass measurement error in 1 min, with no input required besides the mass spectra themselves. The mass measurement accuracy for a set of spectra collected on an LTQ-Velos improved 20-fold from -0.1776 ± 0.0010 m/z to 0.0078 ± 0.0006 m/z after calibration (avg ± 95 % confidence interval). The precision in mass measurement w ...[more]

PMID: 23007965

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Project description:BackgroundSeveral standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-the-art assemblers often did not benefit from this pre-correction step. We found that many error correction tools introduce new errors in reads that overlap highly repetitive DNA regions such as low-complexity patterns or short homopolymers, ultimately leading to a more fragmented assembly.ResultsWe propose BrownieCorrector, an error correction tool for Illumina sequencing data that focuses on the correction of only those reads that overlap short DNA patterns that are highly repetitive in the genome. BrownieCorrector extracts all reads that contain such a pattern and clusters them into different groups using a community detection algorithm that takes into account both the sequence similarity between overlapping reads and their respective paired-end reads. Each cluster holds reads that originate from the same genomic region and hence each cluster can be corrected individually, thus providing a consistent correction for all reads within that cluster.ConclusionsBrownieCorrector is benchmarked using six real Illumina datasets for different eukaryotic genomes. The prior use of BrownieCorrector improves assembly results over the use of uncorrected reads in all cases. In comparison with other error correction tools, BrownieCorrector leads to the best assembly results in most cases even though less than 2% of the reads within a dataset are corrected. Additionally, we investigate the impact of error correction on hybrid assembly where the corrected Illumina reads are supplemented with PacBio data. Our results confirm that BrownieCorrector improves the quality of hybrid genome assembly as well. BrownieCorrector is written in standard C++11 and released under GPL license. BrownieCorrector relies on multithreading to take advantage of multi-core/multi-CPU systems. The source code is available at https://github.com/biointec/browniecorrector .

Dataset Information

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

Publications

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

Similar Datasets

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