Literature DB >> 18428746

Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies.

Erol E Gulcicek1, Christopher M Colangelo, Walter McMurray, Kathryn Stone, Kenneth Williams, Terence Wu, Hongyu Zhao, Heidi Spratt, Alexander Kurosky, Baolin Wu.   

Abstract

In recent years, several proteomic methodologies have been developed that now make it possible to identify, characterize, and comparatively quantify the relative level of expression of hundreds of proteins that are coexpressed in a given cell type or tissue, or that are found in biological fluids such as serum. These advances have resulted from the integration of diverse scientific disciplines including molecular and cellular biology, protein/peptide chemistry, bioinformatics, analytical and bioanalytical chemistry, and the use of instrumental and software tools such as multidimensional electrophoretic and chromatographic separations and mass spectrometry. In this unit, some of the common protein-profiling technologies are reviewed, along with the accompanying data-analysis tools.

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Year:  2005        PMID: 18428746      PMCID: PMC3863626          DOI: 10.1002/0471250953.bi1301s10

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN: 1934-3396


  134 in total

1.  Accurate quantitation of protein expression and site-specific phosphorylation.

Authors:  Y Oda; K Huang; F R Cross; D Cowburn; B T Chait
Journal:  Proc Natl Acad Sci U S A       Date:  1999-06-08       Impact factor: 11.205

2.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

3.  Three-dimensional protein map according to pI, hydrophobicity and molecular mass.

Authors:  Daniel B Wall; Stephen J Parus; David M Lubman
Journal:  J Chromatogr B Analyt Technol Biomed Life Sci       Date:  2002-07-05       Impact factor: 3.205

4.  A mass spectrometric journey into protein and proteome research.

Authors:  Ruedi Aebersold
Journal:  J Am Soc Mass Spectrom       Date:  2003-07       Impact factor: 3.109

5.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology.

Authors:  Michael P Washburn; Ryan Ulaszek; Cosmin Deciu; David M Schieltz; John R Yates
Journal:  Anal Chem       Date:  2002-04-01       Impact factor: 6.986

6.  A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions.

Authors:  Shahid Mian; Graham Ball; Jo Hornbuckle; Finn Holding; James Carmichael; Ian Ellis; Selman Ali; Geng Li; Stephanie McArdle; Colin Creaser; Robert Rees
Journal:  Proteomics       Date:  2003-09       Impact factor: 3.984

7.  Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer.

Authors:  Jinong Li; Zhen Zhang; Jason Rosenzweig; Young Y Wang; Daniel W Chan
Journal:  Clin Chem       Date:  2002-08       Impact factor: 8.327

8.  Profiling receptor tyrosine kinase activation by using Ab microarrays.

Authors:  Ulrik B Nielsen; Mike H Cardone; Anthony J Sinskey; Gavin MacBeath; Peter K Sorger
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-22       Impact factor: 11.205

9.  2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers.

Authors:  Ge Zhou; Hongmei Li; Dianne DeCamp; She Chen; Hongjun Shu; Yi Gong; Michael Flaig; John W Gillespie; Nan Hu; Philip R Taylor; Michael R Emmert-Buck; Lance A Liotta; Emanuel F Petricoin; Yingming Zhao
Journal:  Mol Cell Proteomics       Date:  2002-02       Impact factor: 5.911

10.  Diagnosis of Ovarian Cancer Using Decision Tree Classification of Mass Spectral Data.

Authors:  Antonia Vlahou; John O. Schorge; Betsy W. Gregory; Robert L. Coleman
Journal:  J Biomed Biotechnol       Date:  2003
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  12 in total

Review 1.  Current advantages in the application of proteomics in inflammatory bowel disease.

Authors:  Anna Vaiopoulou; Maria Gazouli; George Theodoropoulos; George Zografos
Journal:  Dig Dis Sci       Date:  2012-06-28       Impact factor: 3.199

2.  LC-MS Based Detection of Differential Protein Expression.

Authors:  Leepika Tuli; Habtom W Ressom
Journal:  J Proteomics Bioinform       Date:  2009-10-02

3.  Proteomic profiling of the rat cerebral cortex in sleep and waking.

Authors:  C Cirelli; M Pfister-Genskow; D McCarthy; R Woodbury; G Tononi
Journal:  Arch Ital Biol       Date:  2009-09       Impact factor: 1.000

Review 4.  Glycoproteomics in neurodegenerative diseases.

Authors:  Hyejin Hwang; Jianpeng Zhang; Kathryn A Chung; James B Leverenz; Cyrus P Zabetian; Elaine R Peskind; Joseph Jankovic; Zhen Su; Aneeka M Hancock; Catherine Pan; Thomas J Montine; Sheng Pan; John Nutt; Roger Albin; Marla Gearing; Richard P Beyer; Min Shi; Jing Zhang
Journal:  Mass Spectrom Rev       Date:  2010 Jan-Feb       Impact factor: 10.946

Review 5.  Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies.

Authors:  Philip Alex; Marjan Gucek; Xuhang Li
Journal:  Inflamm Bowel Dis       Date:  2009-04       Impact factor: 5.325

6.  Systems medicine: the future of medical genomics and healthcare.

Authors:  Charles Auffray; Zhu Chen; Leroy Hood
Journal:  Genome Med       Date:  2009-01-20       Impact factor: 11.117

7.  Efficient Quantitative Comparisons of Plasma Proteomes Using Label-Free Analysis with MaxQuant.

Authors:  Lynn A Beer; Pengyuan Liu; Bonnie Ky; Kurt T Barnhart; David W Speicher
Journal:  Methods Mol Biol       Date:  2017

Review 8.  Molecular signatures of obstructive sleep apnea in adults: a review and perspective.

Authors:  Erna S Arnardottir; Miroslaw Mackiewicz; Thorarinn Gislason; Karen L Teff; Allan I Pack
Journal:  Sleep       Date:  2009-04       Impact factor: 5.849

9.  Albumin-like protein is the major protein constituent of luminal fluid in the human endolymphatic sac.

Authors:  Sung Huhn Kim; Un-Kyoung Kim; Won-Sang Lee; Jinwoong Bok; Jung-Whan Song; Je Kyung Seong; Jae Young Choi
Journal:  PLoS One       Date:  2011-06-29       Impact factor: 3.240

10.  Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates.

Authors:  Yusuke Sasaki; Thomas Eng; Robin A Herbert; Jessica Trinh; Yan Chen; Alberto Rodriguez; John Gladden; Blake A Simmons; Christopher J Petzold; Aindrila Mukhopadhyay
Journal:  Biotechnol Biofuels       Date:  2019-02-27       Impact factor: 6.040

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