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Accurate and sensitive identification of peptides from MS/MS spectra is a very challenging problem in computational shotgun proteomics. To tackle this problem, spectral library search has been one of competitive solutions. However, most existing library search tools were developed on the basis of one peptide per spectrum, which prevents them from working properly on chimeric spectra where two or more peptides are co-fragmented. In this work, we present a new library search tool called ChimST, which is particularly capable of reliably identifying multiple peptides from a chimeric spectrum. It starts with associating each query MS/MS spectrum with MS precursor features. For each precursor feature, there is a list of peptide candidates extracted from an input spectral library. Then, it takes one peptide candidate from each associated feature and scores how well they could collectively interpret the query spectrum. The highest-scoring set of peptide candidates are finally reported as the identification of the query spectrum. Our experimental tests show that ChimST could significantly outperform the three state-of-the-art library search tools, SpectraST, reSpect, and MSPLIT, in terms of the numbers of both peptide-spectrum matches and unique peptides, especially when the acquisition isolation window is broad.
This article was published in the following journal.
Name: IEEE/ACM transactions on computational biology and bioinformatics
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Lists of material available in a library arranged in order with bibliographical METADATA for the purpose of identification and retrieval.
Development of a library collection, including the determination and coordination of selection policy, assessment of needs of users and potential users, collection use studies, collection evaluation, identification of collection needs, selection of materials, planning for resource sharing, collection maintenance and weeding, and budgeting.
The simultaneous identification of all chromosomes from a cell by fluorescence in situ hybridization (IN SITU HYBRIDIZATION, FLUORESCENCE) with chromosome-specific florescent probes that are discerned by their different emission spectra.
A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.
Collection and analysis of data pertaining to operations of a particular library, library system, or group of independent libraries, with recommendations for improvement and/or ordered plans for further development.
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