A new approach that allows identification of intron-split peptides from mass spectrometric data in genomic databases
We present a new approach that allows the identification of intron-split peptides from mass spectrometric data in genomic databases. Our algorithm uses small regions of peptide sequence information which are automatically deduced from de novo amino acid sequence predictions together with the molecul...
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| Veröffentlicht in: | FEBS letters 2004-03, Vol.562 (1-3), p.202-206 |
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| container_title | FEBS letters |
| container_volume | 562 |
| creator | Allmer, Jens Markert, Christine Stauber, Einar J. Hippler, Michael |
| description | We present a new approach that allows the identification of intron-split peptides from mass spectrometric data in genomic databases. Our algorithm uses small regions of peptide sequence information which are automatically deduced from de novo amino acid sequence predictions together with the molecular mass information of the precursor ion. The sequence predictions are based on selected collision-induced mass spectrometric fragmentation spectra. Fragments of the predicted amino acid sequence are aligned with each of the six frames of the translated genome and the precursor mass information is used to assemble the corresponding tryptic peptides using the sequence as a matrix. Hereby, intron-split peptides can be gathered and in turn verified by mass spectrometric data interpretation tools such as Sequest. |
| doi_str_mv | 10.1016/S0014-5793(04)00212-1 |
| format | Article |
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Our algorithm uses small regions of peptide sequence information which are automatically deduced from de novo amino acid sequence predictions together with the molecular mass information of the precursor ion. The sequence predictions are based on selected collision-induced mass spectrometric fragmentation spectra. Fragments of the predicted amino acid sequence are aligned with each of the six frames of the translated genome and the precursor mass information is used to assemble the corresponding tryptic peptides using the sequence as a matrix. Hereby, intron-split peptides can be gathered and in turn verified by mass spectrometric data interpretation tools such as Sequest.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>Animals</subject><subject>Chlamydomonas reinhardtii</subject><subject>Databases, Genetic</subject><subject>Genome</subject><subject>Genome data</subject><subject>GPF, genomic peptide finder</subject><subject>Introns</subject><subject>Intron–exon structure</subject><subject>Mass spectrometry</subject><subject>Mass Spectrometry - methods</subject><subject>MS, mass spectrometry</subject><subject>MS/MS, tandem mass spectrometry</subject><subject>Peptides - chemistry</subject><subject>Peptides - genetics</subject><subject>Proteomics</subject><subject>Search algorithm</subject><issn>0014-5793</issn><issn>1873-3468</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1u1TAQhS0EopfCI4C8QrAIzCRO7KxQqVqKVIkFsLYce0KNkjjYvlz17fH9ESzLypqZb-aM5zD2EuEdAnbvvwKgqFrZN29AvAWosa7wEdugkk3ViE49Zpu_yBl7ltJPKLHC_ik7wxaEgLrbsHzBF9pxs64xGHvH853J3ExT2CXuHS3Zj96a7MPCw8j9kmNYqrROPvOV1lyQxMcYZj6blHhayRZiphy95c5kU1r4D1rCfIoHkyg9Z09GMyV6cXrP2ffrq2-XN9Xtl0-fLy9uKytaidVQGzeCsQKFaAc5WttbVKIV4FzfEylUAzhlnGugpBwqcp0aOlnSqpeyOWevj3PL535tKWU9-2RpmsxCYZu0RNlhB_ggiL3Epu7bArZH0MaQUqRRr9HPJt5rBL33RR980fujaxD64IveC7w6CWyHmdy_rpMRBbg5Ajs_0f3_TdXXVx_rQ2VfAHFI77U-HEdROe1vT1En62mx5Hws9mgX_APb_gFoB7J7</recordid><startdate>20040326</startdate><enddate>20040326</enddate><creator>Allmer, Jens</creator><creator>Markert, Christine</creator><creator>Stauber, Einar J.</creator><creator>Hippler, Michael</creator><general>Elsevier B.V</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20040326</creationdate><title>A new approach that allows identification of intron-split peptides from mass spectrometric data in genomic databases</title><author>Allmer, Jens ; Markert, Christine ; Stauber, Einar J. ; Hippler, Michael</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4571-b2adf0ac41445b7fcc9c184540dd99ee818b0d8add300ddd18ed68b678b089773</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Algorithms</topic><topic>Amino Acid Sequence</topic><topic>Animals</topic><topic>Chlamydomonas reinhardtii</topic><topic>Databases, Genetic</topic><topic>Genome</topic><topic>Genome data</topic><topic>GPF, genomic peptide finder</topic><topic>Introns</topic><topic>Intron–exon structure</topic><topic>Mass spectrometry</topic><topic>Mass Spectrometry - methods</topic><topic>MS, mass spectrometry</topic><topic>MS/MS, tandem mass spectrometry</topic><topic>Peptides - chemistry</topic><topic>Peptides - genetics</topic><topic>Proteomics</topic><topic>Search algorithm</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Allmer, Jens</creatorcontrib><creatorcontrib>Markert, Christine</creatorcontrib><creatorcontrib>Stauber, Einar J.</creatorcontrib><creatorcontrib>Hippler, Michael</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEBS letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Allmer, Jens</au><au>Markert, Christine</au><au>Stauber, Einar J.</au><au>Hippler, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A new approach that allows identification of intron-split peptides from mass spectrometric data in genomic databases</atitle><jtitle>FEBS letters</jtitle><addtitle>FEBS Lett</addtitle><date>2004-03-26</date><risdate>2004</risdate><volume>562</volume><issue>1-3</issue><spage>202</spage><epage>206</epage><pages>202-206</pages><issn>0014-5793</issn><eissn>1873-3468</eissn><abstract>We present a new approach that allows the identification of intron-split peptides from mass spectrometric data in genomic databases. 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| ispartof | FEBS letters, 2004-03, Vol.562 (1-3), p.202-206 |
| issn | 0014-5793 1873-3468 |
| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals Complete; Wiley Online Library Journals Frontfile Complete; Wiley Online Library Free Content; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Alma/SFX Local Collection |
| subjects | Algorithms Amino Acid Sequence Animals Chlamydomonas reinhardtii Databases, Genetic Genome Genome data GPF, genomic peptide finder Introns Intron–exon structure Mass spectrometry Mass Spectrometry - methods MS, mass spectrometry MS/MS, tandem mass spectrometry Peptides - chemistry Peptides - genetics Proteomics Search algorithm |
| title | A new approach that allows identification of intron-split peptides from mass spectrometric data in genomic databases |
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