Characterization of the Low Molecular Weight Human Serum Proteome
Radhakrishna S. Tirumalai,King C. Chan,DaRue A. Prieto,Haleem J. Issaq,Thomas P. Conrads,Timothy D. Veenstra +5 more
TLDR
In this paper, a low molecular weight (LMW) serum proteome was extracted from serum and analyzed using microcapillary reversed-phase liquid chromatography coupled with electrospray ionization tandem mass spectrometry.About:
This article is published in Molecular & Cellular Proteomics.The article was published on 2003-10-01 and is currently open access. It has received 830 citations till now. The article focuses on the topics: Proteome & Blood proteins.read more
Citations
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Protein biomarker discovery and validation: the long and uncertain path to clinical utility.
TL;DR: Better understanding of the overall process of biomarker discovery and validation and of the challenges and strategies inherent in each phase should improve experimental study design, in turn increasing the efficiency of biomarkers development and facilitating the delivery and deployment of novel clinical tests.
Journal ArticleDOI
The Human Plasma Proteome A Nonredundant List Developed by Combination of Four Separate Sources
N. Leigh Anderson,Malu Polanski,Rembert Pieper,Tina Gatlin,Radhakrishna S. Tirumalai,Thomas P. Conrads,Timothy D. Veenstra,Joshua N. Adkins,Joel G. Pounds,Richard Fagan,Anna Lobley +10 more
TL;DR: Most major categories of proteins in the human proteome are represented in plasma, with the distribution at successively deeper layers shifting from mostly extracellular to a distribution more like the whole (primarily cellular) proteome.
Journal ArticleDOI
Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.
Gilbert S. Omenn,David J. States,Marcin Adamski,Thomas W. Blackwell,Rajasree Menon,Henning Hermjakob,Rolf Apweiler,Brian B. Haab,Richard J. Simpson,James S. Eddes,Eugene A. Kapp,Robert L. Moritz,Daniel W. Chan,Alex J. Rai,Arie Admon,Ruedi Aebersold,Ruedi Aebersold,Jimmy K. Eng,William S. Hancock,Stanley A. Hefta,Helmut E. Meyer,Young Ki Paik,Jong Shin Yoo,Peipei Ping,Joel G. Pounds,Joshua N. Adkins,Xiaohong Qian,Rong Wang,Valerie C. Wasinger,Chi Yue Wu,Xiaohang Zhao,Rong Zeng,Alexander I. Archakov,Akira Tsugita,Ilan Beer,Akhilesh Pandey,Michael Pisano,Philip C. Andrews,Harald Tammen,David W. Speicher,Samir M. Hanash,Samir M. Hanash +41 more
TL;DR: Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs in the PPP database, and the database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides.
Journal ArticleDOI
Differential exoprotease activities confer tumor-specific serum peptidome patterns
Josep Villanueva,David R. Shaffer,John Philip,Carlos A. Chaparro,Hediye Erdjument-Bromage,Adam B. Olshen,Martin Fleisher,Hans Lilja,Edi Brogi,Jeff Boyd,Marta Sanchez-Carbayo,Eric C. Holland,Carlos Cordon-Cardo,Howard I. Scher,Paul Tempst +14 more
TL;DR: This study provides a direct link between peptide marker profiles of disease and differential protease activity, and the patterns described may have clinical utility as surrogate markers for detection and classification of cancer.
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Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution
TL;DR: The development of quantitative, multiplexed assays for six proteins in plasma that achieve limits of quantitation in the 1–10 ng/ml range with percent coefficients of variation from 3 to 15% without immunoaffinity enrichment of either proteins or peptides is described.
References
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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
TL;DR: The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.
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Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
TL;DR: MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date, identifying 131 proteins with three or more predicted transmembrane domains which allowed us to map the soluble domains of many of the integral membrane proteins.
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Use of proteomic patterns in serum to identify ovarian cancer
Emanuel F. Petricoin,Ali M. Ardekani,Ben A. Hitt,Peter J. Levine,Vincent A. Fusaro,Seth M. Steinberg,Gordon B. Mills,Charles B. Simone,David A. Fishman,Elise C. Kohn,Lance A. Liotta +10 more
TL;DR: A bioinformatics tool was developed and used to identify proteomic patterns in serum that distinguish neoplastic from non-neoplastic disease within the ovary, justifying a prospective population-based assessment of proteomic pattern technology as a screening tool for all stages of ovarian cancer in high-risk and general populations.
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The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer.
Richard Fishel,Mary Kay Lescoe,M.R.S. Rao,Neal G. Copeland,Nancy A. Jenkins,Judy Garber,Michael F. Kane,Richard D. Kolodner +7 more
TL;DR: Data and reports indicating that S. cerevisiae msh2 mutations cause an instability of dinucleotide repeats like those associated with H NPCC suggest that hMSH2 is the HNPCC gene.