ArticleProteome science2007
Methods for peptide identification by spectral comparison.
Article in Proteome science, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Statistical Framework for Identifying Differences in Similar Mass Spectra: Expanding Possibilities for Isomer Identification.Analytical chemistry · 2023Article
- The Emerging Role of uORF-Encoded uPeptides and HLA uLigands in Cellular and Tumor Biology.Cancers · 2022Review
- Characterization of core fucosylation via sequential enzymatic treatments of intact glycopeptides and mass spectrometry analysis.Nature communications · 2022Article
- Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases.International journal of molecular sciences · 2022Review
- Article
- Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma.Cell reports · 2020Article
- Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network.Analytical chemistry · 2020Article
- Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.Analytical chemistry · 2018Article
- Large scale analysis of amino acid substitutions in bacterial proteomics.BMC bioinformatics · 2016Article
- Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments.Journal of the American Society for Mass Spectrometry · 2016Article
- Psoriatic arthritis under a proteomic spotlight: application of novel technologies to advance diagnosis and management.Current rheumatology reports · 2015Review
- Building high-quality assay libraries for targeted analysis of SWATH MS data.Nature protocols · 2015Article
- Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics.Molecular & cellular proteomics : MCP · 2014Article
- Comparative analysis of mass spectral similarity measures on peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry.Computational and mathematical methods in medicine · 2013Article
- Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry.BMC bioinformatics · 2011Article
- An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure.Bioinformatics (Oxford, England) · 2011Article
- Fast parallel tandem mass spectral library searching using GPU hardware acceleration.Journal of proteome research · 2011Article
- Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.Nature methods · 2011Article
- On the accuracy and limits of peptide fragmentation spectrum prediction.Analytical chemistry · 2011Article
- A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language.Genome biology · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandem mass spectrometry followed by database search is currently the predominant technology for peptide sequencing in shotgun proteomics experiments. Most methods compare experimentally observed spectra to the theoretical spectra predicted from the sequences in protein databases. There is a growing interest, however, in comparing unknown experimental spectra to a library of previously identified spectra. This approach has the advantage of taking into account instrument-dependent factors and peptide-specific differences in fragmentation probabilities. It is also computationally more efficient for high-throughput proteomics studies.
resultsThis paper investigates computational issues related to this spectral comparison approach. Different methods have been empirically evaluated over several large sets of spectra. First, we illustrate that the peak intensities follow a Poisson distribution. This implies that applying a square root transform will optimally stabilize the peak intensity variance. Our results show that the square root did indeed outperform other transforms, resulting in improved accuracy of spectral matching. Second, different measures of spectral similarity were compared, and the results illustrated that the correlation coefficient was most robust. Finally, we examine how to assemble multiple spectra associated with the same peptide to generate a synthetic reference spectrum. Ensemble averaging is shown to provide the best combination of accuracy and efficiency.
conclusionOur results demonstrate that when combined, these methods can boost the sensitivity and specificity of spectral comparison. Therefore they are capable of enhancing and complementing existing tools for consistent and accurate peptide identification.
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Registered trials
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