Dataset Information

RAId_DbS: peptide identification using database searches with realistic statistics.

ABSTRACT: The key to mass-spectrometry-based proteomics is peptide identification. A major challenge in peptide identification is to obtain realistic E-values when assigning statistical significance to candidate peptides.Using a simple scoring scheme, we propose a database search method with theoretically characterized statistics. Taking into account possible skewness in the random variable distribution and the effect of finite sampling, we provide a theoretical derivation for the tail of the score distribution. For every experimental spectrum examined, we collect the scores of peptides in the database, and find good agreement between the collected score statistics and our theoretical distribution. Using Student's t-tests, we quantify the degree of agreement between the theoretical distribution and the score statistics collected. The T-tests may be used to measure the reliability of reported statistics. When combined with reported P-value for a peptide hit using a score distribution model, this new measure prevents exaggerated statistics. Another feature of RAId_DbS is its capability of detecting multiple co-eluted peptides. The peptide identification performance and statistical accuracy of RAId_DbS are assessed and compared with several other search tools. The executables and data related to RAId_DbS are freely available upon request.

SUBMITTER: Alves G

PROVIDER: S-EPMC2211744 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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RAId_DbS: peptide identification using database searches with realistic statistics.

Alves Gelio G Ogurtsov Aleksey Y AY Yu Yi-Kuo YK

Biology direct 20071025

<h4>Background</h4>The key to mass-spectrometry-based proteomics is peptide identification. A major challenge in peptide identification is to obtain realistic E-values when assigning statistical significance to candidate peptides.<h4>Results</h4>Using a simple scoring scheme, we propose a database search method with theoretically characterized statistics. Taking into account possible skewness in the random variable distribution and the effect of finite sampling, we provide a theoretical derivati ...[more]

PMID: 17961253

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Project description:MotivationThe BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar.ResultsWe developed a new version of the MegaBLAST module of BLAST that does the initial phase of finding short seeds for matches by searching a database index. We also developed a program makembindex that preprocesses the database into a data structure for rapid seed searching. We show that the new 'indexed MegaBLAST' is faster than the 'non-indexed' version for most practical uses. We show that indexed MegaBLAST is faster than miBLAST, another implementation of BLAST nucleotide searching with a preprocessed database, for most of the 200 queries we tested. To deploy indexed MegaBLAST as part of NCBI'sWeb BLAST service, the storage of databases and the queueing mechanism were modified, so that some machines are now dedicated to serving queries for a specific database. The response time for such Web queries is now faster than it was when each computer handled queries for multiple databases.AvailabilityThe code for indexed MegaBLAST is part of the blastn program in the NCBI C++ toolkit. The preprocessor program makembindex is also in the toolkit. Indexed MegaBLAST has been used in production on NCBI's Web BLAST service to search one version of the human and mouse genomes since October 2007. The Linux command-line executables for blastn and makembindex, documentation, and some query sets used to carry out the tests described below are available in the directory: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/indexed_megablast [corrected]Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

RAId_DbS: peptide identification using database searches with realistic statistics.

Publications

RAId_DbS: peptide identification using database searches with realistic statistics.

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