CyberinfraV1, Main, Merge, bibRecord, 000323

MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach

Identifieur interne : 000323 ( Main/Merge ); précédent : 000322; suivant : 000324

MRMPath 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.

RBID : PMC:3570921

Abstract

Quantitative proteomics applications in mass spectrometry depend on the knowledge of the mass-to-charge ratio (m/z) 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 in silico 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.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570921

DOI: 10.1155/2013/527295
PubMed: 23424586
PubMed Central: 3570921

Links toward previous steps (curation, corpus...)

to stream Pmc, to step Corpus: 000475
to stream Pmc, to step Curation: 000475
to stream Pmc, to step Checkpoint: 000302
to stream Ncbi, to step Merge: 000392
to stream Ncbi, to step Curation: 000392
to stream Ncbi, to step Checkpoint: 000392

Links to Exploration step

PMC:3570921

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach</title>
<author><name sortKey="Crasto, Chiquito" sort="Crasto, Chiquito" uniqKey="Crasto C" 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>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">23424586</idno>
<idno type="pmc">3570921</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570921</idno>
<idno type="RBID">PMC:3570921</idno>
<idno type="doi">10.1155/2013/527295</idno>
<date when="2013">2013</date>
<idno type="wicri:Area/Pmc/Corpus">000475</idno>
<idno type="wicri:Area/Pmc/Curation">000475</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000302</idno>
<idno type="wicri:Area/Ncbi/Merge">000392</idno>
<idno type="wicri:Area/Ncbi/Curation">000392</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000392</idno>
<idno type="wicri:doubleKey">1687-8027:2013:Crasto C:mrmpath:and:mrmutation</idno>
<idno type="wicri:Area/Main/Merge">000323</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach</title>
<author><name sortKey="Crasto, Chiquito" sort="Crasto, Chiquito" uniqKey="Crasto C" 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>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Merge

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000323 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000323 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Ticri/CIDE
   |area=    CyberinfraV1
   |flux=    Main
   |étape=   Merge
   |type=    RBID
   |clé=     PMC:3570921
   |texte=   MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i   -Sk "pubmed:23424586" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd   \
       | NlmPubMed2Wicri -a CyberinfraV1

This area was generated with Dilib version V0.6.25.
Data generation: Thu Oct 27 09:30:58 2016. Site generation: Sun Mar 10 23:08:40 2024

	Serveur d'exploration Cyberinfrastructure
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration Cyberinfrastructure

MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach

MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach

Source :

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki