A Functional Proteomic Method for Biomarker Discovery
Publication Date
July 19, 2011
Journal
PLOS ONE
Authors
Fred Reynolds, Nivedha Panneer, Christopher M. Tutino, Michael Wu, et al
Volume
6
Issue
7
Pages
e22471
DOI
https://dx.plos.org/10.1371/journal.pone.0022471
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0022471
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21811618
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139652
Europe PMC
http://europepmc.org/abstract/MED/21811618
Web of Science
000292929500070
Scopus
79960472731
Mendeley
http://www.mendeley.com/research/functional-proteomic-method-biomarker-discovery
Events
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Mendeley | Further Information

{"title"=>"A functional proteomic method for biomarker discovery", "type"=>"journal", "authors"=>[{"first_name"=>"Fred", "last_name"=>"Reynolds", "scopus_author_id"=>"7102898750"}, {"first_name"=>"Nivedha", "last_name"=>"Panneer", "scopus_author_id"=>"43361669000"}, {"first_name"=>"Christopher M.", "last_name"=>"Tutino", "scopus_author_id"=>"43361781700"}, {"first_name"=>"Michael", "last_name"=>"Wu", "scopus_author_id"=>"9844831700"}, {"first_name"=>"William R.", "last_name"=>"Skrabal", "scopus_author_id"=>"43361887500"}, {"first_name"=>"Christopher", "last_name"=>"Moskaluk", "scopus_author_id"=>"7003905170"}, {"first_name"=>"Kimberly A.", "last_name"=>"Kelly", "scopus_author_id"=>"56697831000"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79960472731", "pmid"=>"21811618", "sgr"=>"79960472731", "doi"=>"10.1371/journal.pone.0022471", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "pui"=>"362161266"}, "id"=>"41db72b8-b7d7-3cbc-ac71-2c7ad26ddd1c", "abstract"=>"The sequencing of the human genome holds out the hope for personalized medicine, but it is clear that analysis of DNA or RNA content alone is not sufficient to understand most disease processes. Proteomic strategies that allow unbiased identification of proteins and their post-transcriptional and -translation modifications are an essential complement to genomic strategies. However, the enormity of the proteome and limitations in proteomic methods make it difficult to determine the targets that are particularly relevant to human disease. Methods are therefore needed that allow rational identification of targets based on function and relevance to disease. Screening methodologies such as phage display, SELEX, and small-molecule combinatorial chemistry have been widely used to discover specific ligands for cells or tissues of interest, such as tumors. Those ligands can be used in turn as affinity probes to identify their cognate molecular targets when they are not known in advance. Here we report an easy, robust and generally applicable approach in which phage particles bearing cell- or tissue-specific peptides serve directly as the affinity probes for their molecular targets. For proof of principle, the method successfully identified molecular binding partners, three of them novel, for 15 peptides specific for pancreatic cancer.", "link"=>"http://www.mendeley.com/research/functional-proteomic-method-biomarker-discovery", "reader_count"=>28, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>12, "Student > Ph. D. Student"=>5, "Other"=>4, "Student > Master"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>12, "Student > Ph. D. Student"=>5, "Other"=>4, "Student > Master"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>5, "Veterinary Science and Veterinary Medicine"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Czech Republic"=>1, "United States"=>2, "China"=>1, "Brazil"=>1, "France"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/755457"], "description"=>"<p>A) Specificity of each clone as measured by ELISA. Clones in white were insufficiently specific (>1) and therefore, not used. B) Weighted sum of the specificity and affinity of each clone. Clones in white were not investigated further.</p>", "links"=>[], "tags"=>["clones"], "article_id"=>425829, "categories"=>["Cancer", "Biochemistry"], "users"=>["Fred Reynolds", "Nivedha Panneer", "Christopher M. Tutino", "Michael Wu", "William R. Skrabal", "Christopher Moskaluk", "Kimberly A. Kelly"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022471.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ranking_of_clones_for_selection_/425829", "title"=>"Ranking of clones for selection.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/755669"], "description"=>"<p>A) Western blot of the protein that binds to clone 8, probed using anti-pyruvate kinase M2 antibody. B) ELISA of clone 8 incubated with purified pyruvate kinase M2, or with BSA or recombinant annexin A2 as negative controls. C) Western blot of cell fractionation using anti-pyruvate kinase M2 antibody D) ELISA on intact, non-permeabilized L3.6pl cells with anti-pyruvate kinase M2 antibody. E) Western blot of clone 15 associated protein probed with anti annexin A2 antibody. E) ELISA showing binding of clone 15 to annexin A2 protein. F) Western blot of cell fractionation using anti annexin A2 antibody. G) ELISA on intact, non-permeabilized L3.6pl cells with anti-Annexin A2 antibody.</p>", "links"=>[], "tags"=>["affinity", "phage"], "article_id"=>426038, "categories"=>["Cancer", "Biochemistry"], "users"=>["Fred Reynolds", "Nivedha Panneer", "Christopher M. Tutino", "Michael Wu", "William R. Skrabal", "Christopher Moskaluk", "Kimberly A. Kelly"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022471.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_affinity_partner_for_phage_clones_/426038", "title"=>"Validation of affinity partner for phage clones.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:39:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/755563"], "description"=>"<p>Elution sample from Panc 8 (A) and Panc 15 (C) were run on SDS/PAGE then stained with coomassie. Sequence of pyruvate kinase M2 (B) and Annexin A2 (D), with peptides recovered from tryptic digest of the band from (A) and (C) in red.</p>", "links"=>[], "tags"=>["spectroscopic"], "article_id"=>425932, "categories"=>["Cancer", "Biochemistry"], "users"=>["Fred Reynolds", "Nivedha Panneer", "Christopher M. Tutino", "Michael Wu", "William R. Skrabal", "Christopher Moskaluk", "Kimberly A. Kelly"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022471.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pulldown_and_mass_spectroscopic_analysis_/425932", "title"=>"Pulldown and mass spectroscopic analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:39:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/755867"], "description"=>"<p>Listing of the phage clones, their binding peptide sequence, and their associated targeted protein.</p>", "links"=>[], "tags"=>["phage", "binding", "peptide", "targeted"], "article_id"=>426230, "categories"=>["Cancer", "Biochemistry"], "users"=>["Fred Reynolds", "Nivedha Panneer", "Christopher M. Tutino", "Michael Wu", "William R. Skrabal", "Christopher Moskaluk", "Kimberly A. Kelly"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022471.t001", "stats"=>{"downloads"=>15, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Listing_of_the_phage_clones_their_binding_peptide_sequence_and_their_associated_targeted_protein_/426230", "title"=>"Listing of the phage clones, their binding peptide sequence, and their associated targeted protein.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 16:40:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/755764"], "description"=>"<p>Values are pathologist's scoring of number of cells stained (0–3) and intensity of staining (0–3) multiplied together. A) Representative tumor section stained for plectin. Note the membrane staining. B) Pathologist's scoring of human cancer biopsy specimens stained for plectin. C) Representative PDAC tumor biopsy section stained for pyruvate kinase M2. D) Pathologist's scoring of pyruvate kinase M2 stained human cancer biopsy tissue sections.</p>", "links"=>[], "tags"=>["microarray"], "article_id"=>426138, "categories"=>["Cancer", "Biochemistry"], "users"=>["Fred Reynolds", "Nivedha Panneer", "Christopher M. Tutino", "Michael Wu", "William R. Skrabal", "Christopher Moskaluk", "Kimberly A. Kelly"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022471.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tissue_microarray_data_/426138", "title"=>"Tissue microarray data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:40:15"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
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Relative Metric

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