Linked Life Data

21250827

Source:http://linkedlifedata.com/resource/pubmed/id/21250827

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1-2
pubmed:dateCreated
2011-1-31
pubmed:abstractText
High-throughput (HTP) proteomics studies generate large amounts of data. Interpretation of these data requires effective approaches to distinguish noise from biological signal, particularly as instrument and computational capacity increase and studies become more complex. Resolving this issue requires validated and reproducible methods and models, which in turn requires complex experimental and computational standards. The absence of appropriate standards and data sets for validating experimental and computational workflows hinders the development of HTP proteomics methods. Most protein standards are simple mixtures of proteins or peptides, or undercharacterized reference standards in which the identity and concentration of the constituent proteins is unknown. The Seattle Children's 200 (SC-200) proposed proteomics standard mixture is the next step toward developing realistic, fully characterized HTP proteomics standards. The SC-200 exhibits a unique modular design to extend its functionality, and consists of 200 proteins of known identities and molar concentrations from 6 microbial genomes, distributed into 10 molar concentration tiers spanning a 1,000-fold range. We describe the SC-200's design, potential uses, and initial characterization. We identified 84% of SC-200 proteins with an LTQ-Orbitrap and 65% with an LTQ-Velos (false discovery rate?=?1% for both). There were obvious trends in success rate, sequence coverage, and spectral counts with protein concentration; however, protein identification, sequence coverage, and spectral counts vary greatly within concentration levels.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-12141667, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-12143966, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-14976030, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-15107238, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-15703482, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-15958392, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-16603360, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-16901220, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-17121779, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-17195840, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-17890649, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-18092908, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-19068132, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-19448641, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-19594426, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-19892172, http://linkedlifedata.com/resource/pubmed/commentcorrection/21250827-20391536
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:issn
1557-8100
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
15
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
73-82
pubmed:dateRevised
2011-9-26
pubmed:meshHeading
pubmed:articleTitle
Design and initial characterization of the SC-200 proteomics standard mixture.
pubmed:affiliation
Seattle Children's Research Institute, Bioinformatics and High-throughput Analysis Laboratory, Seattle Children's Research Institute, High-throughput Analysis Core, Seattle, Washington 98109, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural