MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach
Identifieur interne : 000302 ( Pmc/Checkpoint ); précédent : 000301; suivant : 000303MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach
Auteurs : Chiquito Crasto [États-Unis] ; Chandrahas Narne [États-Unis] ; Mikako Kawai [États-Unis] ; Landon Wilson [États-Unis] ; Stephen Barnes [États-Unis]Source :
- Advances in Bioinformatics [ 1687-8027 ] ; 2013.
Abstract
Quantitative proteomics applications in mass spectrometry depend on the knowledge of the mass-to-charge ratio (
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DOI: 10.1155/2013/527295
PubMed: 23424586
PubMed Central: 3570921
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first="Chiquito" last="Crasto">Chiquito Crasto</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Narne, Chandrahas" sort="Narne, Chandrahas" uniqKey="Narne C" first="Chandrahas" last="Narne">Chandrahas Narne</name><affiliation wicri:level="2"><nlm:aff id="I2">Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Kawai, Mikako" sort="Kawai, Mikako" uniqKey="Kawai M" first="Mikako" last="Kawai">Mikako Kawai</name><affiliation wicri:level="2"><nlm:aff id="I3">Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Wilson, Landon" sort="Wilson, Landon" uniqKey="Wilson L" first="Landon" last="Wilson">Landon Wilson</name><affiliation wicri:level="2"><nlm:aff id="I4">Centers for Nutrient-Gene Interactions, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Centers for Nutrient-Gene Interactions, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Barnes, Stephen" sort="Barnes, Stephen" uniqKey="Barnes S" first="Stephen" last="Barnes">Stephen Barnes</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I4">Centers for Nutrient-Gene Interactions, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Centers for Nutrient-Gene Interactions, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I5">Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author></analytic><series><title level="j">Advances in Bioinformatics</title><idno type="ISSN">1687-8027</idno><idno type="eISSN">1687-8035</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Quantitative proteomics applications in mass spectrometry depend on the knowledge of the mass-to-charge ratio (<italic>m/z</italic>) values of proteotypic peptides for the proteins under study and their product ions. MRMPath and MRMutation, web-based bioinformatics software that are platform independent, facilitate the recovery of this information by biologists. MRMPath utilizes publicly available information related to biological pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. All the proteins involved in pathways of interest are recovered and processed <italic>in silico</italic> to extract information relevant to quantitative mass spectrometry analysis. Peptides may also be subjected to automated BLAST analysis to determine whether they are proteotypic. MRMutation catalogs and makes available, following processing, known (mutant) variants of proteins from the current UniProtKB database. All these results, available via the web from well-maintained, public databases, are written to an Excel spreadsheet, which the user can download and save. MRMPath and MRMutation can be freely accessed. As a system that seeks to allow two or more resources to interoperate, MRMPath represents an advance in bioinformatics tool development. As a practical matter, the MRMPath automated approach represents significant time savings to researchers.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hillenkamp, F" uniqKey="Hillenkamp F">F Hillenkamp</name></author><author><name sortKey="Karas, M" uniqKey="Karas M">M Karas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fenn, Jb" uniqKey="Fenn J">JB Fenn</name></author><author><name sortKey="Mann, M" uniqKey="Mann M">M Mann</name></author><author><name sortKey="Meng, Ck" uniqKey="Meng C">CK Meng</name></author><author><name sortKey="Wong, Sf" uniqKey="Wong S">SF Wong</name></author><author><name sortKey="Whitehouse, Cm" uniqKey="Whitehouse C">CM Whitehouse</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Diz, Ap" uniqKey="Diz A">AP Diz</name></author><author><name sortKey="Carvajal Rodriguez, A" uniqKey="Carvajal Rodriguez A">A Carvajal-Rodríguez</name></author><author><name sortKey="Skibinski, Dof" uniqKey="Skibinski D">DOF Skibinski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ransohoff, Df" uniqKey="Ransohoff D">DF Ransohoff</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gerber, Sa" uniqKey="Gerber S">SA Gerber</name></author><author><name sortKey="Rush, J" uniqKey="Rush J">J Rush</name></author><author><name sortKey="Stemman, O" uniqKey="Stemman O">O Stemman</name></author><author><name sortKey="Kirschner, Mw" uniqKey="Kirschner M">MW Kirschner</name></author><author><name sortKey="Gygi, Sp" uniqKey="Gygi S">SP Gygi</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Conrad, Df" uniqKey="Conrad D">DF Conrad</name></author><author><name sortKey="Keebler, Jem" uniqKey="Keebler J">JEM Keebler</name></author><author><name sortKey="Depristo, Ma" uniqKey="Depristo M">MA Depristo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Buetow, Kh" uniqKey="Buetow K">KH Buetow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cannataro, M" uniqKey="Cannataro M">M Cannataro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Litwin, W" uniqKey="Litwin W">W Litwin</name></author><author><name sortKey="Mark, L" uniqKey="Mark L">L Mark</name></author><author><name sortKey="Roussopoulos, N" uniqKey="Roussopoulos N">N Roussopoulos</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Adv Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">Adv Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">ABI</journal-id><journal-title-group><journal-title>Advances in Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1687-8027</issn><issn pub-type="epub">1687-8035</issn><publisher><publisher-name>Hindawi Publishing Corporation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23424586</article-id><article-id pub-id-type="pmc">3570921</article-id><article-id pub-id-type="doi">10.1155/2013/527295</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Crasto</surname><given-names>Chiquito</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Narne</surname><given-names>Chandrahas</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kawai</surname><given-names>Mikako</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wilson</surname><given-names>Landon</given-names></name><xref ref-type="aff" rid="I4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Barnes</surname><given-names>Stephen</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="aff" rid="I3"><sup>3</sup></xref><xref ref-type="aff" rid="I4"><sup>4</sup></xref><xref ref-type="aff" rid="I5"><sup>5</sup></xref></contrib></contrib-group><aff id="I1"><sup>1</sup>Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA</aff><aff id="I2"><sup>2</sup>Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA</aff><aff id="I3"><sup>3</sup>Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA</aff><aff id="I4"><sup>4</sup>Centers for Nutrient-Gene Interactions, University of Alabama at Birmingham, Birmingham, AL 35294, USA</aff><aff id="I5"><sup>5</sup>Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA</aff><author-notes><corresp id="cor1">*Chiquito Crasto: <email>chiquito@uab.edu</email></corresp><fn fn-type="other"><p>Academic Editor: Erchin Serpedin</p></fn></author-notes><pub-date pub-type="ppub"><year>2013</year></pub-date><pub-date pub-type="epub"><day>29</day><month>1</month><year>2013</year></pub-date><volume>2013</volume><elocation-id>527295</elocation-id><history><date date-type="received"><day>23</day><month>9</month><year>2012</year></date><date date-type="rev-recd"><day>20</day><month>12</month><year>2012</year></date><date date-type="accepted"><day>20</day><month>12</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2013 Chiquito Crasto et al.</copyright-statement><copyright-year>2013</copyright-year><license license-type="open-access"><license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Quantitative proteomics applications in mass spectrometry depend on the knowledge of the mass-to-charge ratio (<italic>m/z</italic>) values of proteotypic peptides for the proteins under study and their product ions. MRMPath and MRMutation, web-based bioinformatics software that are platform independent, facilitate the recovery of this information by biologists. MRMPath utilizes publicly available information related to biological pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. All the proteins involved in pathways of interest are recovered and processed <italic>in silico</italic> to extract information relevant to quantitative mass spectrometry analysis. Peptides may also be subjected to automated BLAST analysis to determine whether they are proteotypic. MRMutation catalogs and makes available, following processing, known (mutant) variants of proteins from the current UniProtKB database. All these results, available via the web from well-maintained, public databases, are written to an Excel spreadsheet, which the user can download and save. MRMPath and MRMutation can be freely accessed. As a system that seeks to allow two or more resources to interoperate, MRMPath represents an advance in bioinformatics tool development. As a practical matter, the MRMPath automated approach represents significant time savings to researchers.</p></abstract></article-meta></front><floats-group><fig id="fig1" orientation="portrait" position="float"><label>Figure 1</label><caption><p>The figure represents the pathway for the citrate tricarboxylic acid cycle for humans as seen at the KEGG resource. The components, proteins, and reagents, highlighted in green, are those involved in the pathway for humans. The components not highlighted are part of the generic TCA cycle pathway. If another species is selected then only those components that contribute to the pathway are highlighted. The figure is a screen capture from the URL, <ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/kegg-bin/show_pathway?org_name=mmu&mapno=00062">http://www.genome.jp/kegg-bin/show_pathway?org_name=mmu&mapno=00062</ext-link>.</p></caption><graphic xlink:href="ABI2013-527295.001"></graphic></fig><fig id="fig2" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Front page of the Targeted Metabolomics and Proteomics Laboratory website. This is the home page for MRMPath and MRMutation. The three input choices for MRMPath—processing of peptides of proteins involved in biological pathways via KEGG, through Accession IDs in UniProt and direct input of a protein sequence—are illustrated.</p></caption><graphic xlink:href="ABI2013-527295.002"></graphic></fig><fig id="fig3" orientation="portrait" position="float"><label>Figure 3</label><caption><p>A screen capture of MRMPath results (truncated) shows the peptides for a chosen protein (isocitrate dehydrogenase) from the TCA cycle pathway. The peptides are a result of a tryptic digest, the precursor ion values and the b- and y-ions whose masses are greater than that of the precursor ion identified. The link towards the top of the page allows users to download the processing result to an Excel spreadsheet. The buttons that allow BLAST searching of individual peptides as well all peptides from the chosen protein are also illustrated in the figure.</p></caption><graphic xlink:href="ABI2013-527295.003"></graphic></fig><fig id="fig4" orientation="portrait" position="float"><label>Figure 4</label><caption><p>The result of a BLAST search of the tryptic peptide, the first peptide from <xref ref-type="fig" rid="fig3">Figure 3</xref>, shows that no results are found. The <italic>m/z</italic> for the parent ion of this peptide is also illustrated. If sequences similar to the peptide were identified, the top ten results would appear with links back to the GenBank resource for each similar sequence in the third column in the figure.</p></caption><graphic xlink:href="ABI2013-527295.004"></graphic></fig><fig id="fig5" orientation="portrait" position="float"><label>Figure 5</label><caption><p> (a) The user interface for MRMutation. A user can input a free text search of the Accession ID of a UniProt entry. (b) The results (truncated) of a search in the interface identified records with the keyword “p53.” (c) Clicking the first link results in the creation of a tryptic digest of the protein identified through Accession ID P04637. The mutated amino acid residues are highlighted in the tryptic peptide sequence, along with the <italic>m/z</italic> of the parent peptide ion.</p></caption><graphic xlink:href="ABI2013-527295.005"></graphic></fig></floats-group></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Alabama</li></region></list><tree><country name="États-Unis"><region name="Alabama"><name sortKey="Crasto, Chiquito" sort="Crasto, Chiquito" uniqKey="Crasto C" first="Chiquito" last="Crasto">Chiquito Crasto</name></region><name sortKey="Barnes, Stephen" sort="Barnes, Stephen" uniqKey="Barnes S" first="Stephen" last="Barnes">Stephen Barnes</name><name sortKey="Barnes, Stephen" sort="Barnes, Stephen" uniqKey="Barnes S" first="Stephen" last="Barnes">Stephen Barnes</name><name sortKey="Barnes, Stephen" sort="Barnes, Stephen" uniqKey="Barnes S" first="Stephen" last="Barnes">Stephen Barnes</name><name sortKey="Barnes, Stephen" sort="Barnes, Stephen" uniqKey="Barnes S" first="Stephen" last="Barnes">Stephen Barnes</name><name sortKey="Kawai, Mikako" sort="Kawai, Mikako" uniqKey="Kawai M" first="Mikako" last="Kawai">Mikako Kawai</name><name sortKey="Narne, Chandrahas" sort="Narne, Chandrahas" uniqKey="Narne C" first="Chandrahas" last="Narne">Chandrahas Narne</name><name sortKey="Wilson, Landon" sort="Wilson, Landon" uniqKey="Wilson L" first="Landon" last="Wilson">Landon Wilson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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