Articles

Identification of Tumor-Associated Proteins in Well Differentiated Laryngeal Squamous Cell Carcinoma by Proteomics

This study established two-dimensional gel electrophoresis (2-DE) profiles for human well-differentiated laryngeal squamous cell carcinoma tissue and paired normal mucosa epithelia tissue and identified protei...

Authors: Jian-rong Zhou, Zhong-xue Fu, Jie Li, Lian-zhi Wei and Jun-cai Li

Liquid Chromatography/Mass Spectrometry (LC/MS)-Based Glycoproteomics Technologies for Cancer Biomarker Discovery

Biomarker discovery is a major objective of clinical proteomics; molecular biomarkers allow for detection of early-stage human diseases, especially cancer, and for monitoring their progression and/or regressio...

Authors: Hiroyuki Kaji and Toshiaki Isobe

An Organized Effort is Needed to Fast Track the Development of Cancer Biomarkers

Authors: Sam Hanash

Proteomic Analysis of Two Non-Bronchoscopic Methods of Sampling the Lungs of Patients with the Acute Respiratory Distress Syndrome (ARDS)

The collection of lung fluid using a suction catheter (s-Cath) and non-bronchoscopic bronchoalveolar lavage (mini-BAL) are two minimally invasive methods of sampling the distal airspaces in patients with the a...

Authors: Dong W. Chang, Giuseppe Colucci, Tomas Vaisar, Trevor King, Shinichi Hayashi, Gustavo Matute-Bello, Roger Bumgarner, Jay Heinecke, Thomas R. Martin and Guido M. Domenighetti

Proteomic Profiling of Ovarian Cancer Plasma using Immunoaffinity Depleted Plasma and Two-Dimensional PAGE

The aim of this study was to evaluate a multiple immunoaffinity protein depletion (multiple affinity removal system, MARS) pre-treatment strategy with subsequent two-dimensional polyacrylamide gel electrophore...

Authors: Karen T. Oliva, Mustafa Ayhan, Gillian Barker, Nicole L. Dellios, Michael A. Quinn and Gregory E. Rice

Proteomic Studies of Saliva: A Proposal for a Standardized Handling of Clinical Samples

In recent years, differential analysis of proteins from human saliva, i.e., proteomic analysis, has received much attention mainly due to its unstressful sampling and its great potential for biomarker research...

Authors: François Chevalier, Christophe Hirtz, Sandrine Chay, Frédéric Cuisinier, Nicolas Sommerer, Michel Rossignol and Dominique Deville de Périère

Identification and Validation of Proteinase 3 and Latent Matrix-Metalloproteinase 9 as Potential Biomarkers for Chronic Lung Transplant Rejection

This study examined potential biomarkers for the diagnosis and early detection of chronic allograft rejection after lung transplantation.

Authors: Yan Zhang, Christine H. Wendt, Marshall I. Hertz and Gary L. Nelsestuen

Protein expression analysis ofChlamydia pneumoniae persistence by combined surface-enhanced laser desorption ionization time-of-flight mass spectrometry and two-dimensional polyacrylamide gel electrophoresis

The aim of this study was to examine the protein expression profiles of persistentChlamydia pneumoniae by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) and surface-enhanced laser desorption ionizat...

Authors: Sanghamitra Mukhopadhyay, Saeed A. Jortani, Roland Valdes, Christine Q. Simmons, Erin D. Sullivan, Richard D. Miller and James T. Summersgill

Comparison of protein expression lists from mass spectrometry of human blood fluids using exact peptide sequences versus BLAST

The proteins in blood were all first expressed as mRNAs from genes within cells. There are databases of human proteins that are known to be expressed as mRNA in human cells and tissues. Proteins identified fro...

Authors: Peihong Zhu, Peter Bowden, Voitek Pendrak, Herbert Thiele, Du Zhang, Michael Siu, Eleftherios P. Diamandis and John Marshall

Altered proteome profiles in maternal plasma in pregnancies with fetal growth restriction

Fetal growth restriction (FGR) affects 3–5% of pregnancies and is associated with increased perinatal morbidity and mortality. Currently, there is no reliable biochemical test to differentiate a pathological F...

Authors: Madhulika B. Gupta, Maxim D. Seferovic, Suya Liu, Robert J. Gratton, Amanda Doherty-Kirby, Gilles A. Lajoie and Victor K. M. Han

Genistein-induced proteome changes in the human endometrial carcinoma cell line, ishikawa

Epidemiological studies have shown that Asian populations display a lower incidence of hormone-dependant cancers, cardiovascular disease, osteoporosis, and menopausal ailments compared to Western societies. Av...

Authors: Nicki Konstantakopoulos, Martin R. Larsen, Ian G. Campbell, Michael A. Quinn, Mark S. Baker, Harry M. Georgiou and Gregory E. Rice

Comparison between surface and bead-based MALDI profiling technologies using a single bioinformatics algorithm

In this manuscript, we compared serum profiles obtained with two related technologies, SELDI-TOF and Clinprot, using a single bioinformatic algorithm. These two approaches rely on mass spectrometry to detect p...

Authors: Christelle Reynès, Stéphane Roche, Laurent Tiers, Robert Sabatier, Patrick Jouin, Nicolas Molinari and Sylvain Lehmann

Laser-induced dissociation of phosphorylated peptides using matrix assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Reversible phosphorylation is one of the most important posttranslational modifications of cellular proteins. Mass spectrometry is a widely used technique in the characterization of phosphorylated proteins and...

Authors: Dongxia Wang, Philip A. Cole and Robert J. Cotter

Cancer proteomics

The future of cancer diagnostics will be based on a panel of proteomic biomarkers. They could be used to detect cancer at an early stage, to predict and to direct therapies. Enzymes and related proteins are im...

Authors: Daniel W. Chan and Shu-Ling Liang

Salivary protein profiling in type I diabetes using two-dimensional electrophoresis and mass spectrometry

Owing to its noninvasive collection, saliva is considered as a potent diagnostic fluid. The goal of this study was to investigate the modification of the salivary proteome occurring in type 1 diabetes to highl...

Authors: Christophe Hirtz, François Chevalier, Nicolas Sommerer, Isabelle Raingeard, Jacques Bringer, Michel Rossignol and Dominique Deville de Périere

Mass determination of major plasma proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) serves as a rapid and accurate means to determine masses of proteins independent of their shapes or interactions with...

Authors: Glen L. Hortin and Alan T. Remaley

Assessment of protein stability in cerebrospinal fluid using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry protein profiling

Recent studies have evaluated proper acquisition and storage procedures for the use of serum or plasma for mass spectrometry (MS)-based proteomics. The present study examines the proteome stability of human ce...

Authors: Srikanth Ranganathan, Anna Polshyna, Georgina Nicholl, James Lyons-Weiler and Robert Bowser

Comparison of methods to examine the endogenous peptides of fetal calf serum

There is a great desire to relate the patterns of endogenous peptides in blood to human disease and drug response. The best practices for the preparation of blood fluids for analysis are not clear and also rel...

Authors: Declan Williams, Peihong Zhu, Peter Bowden, Catherine Stacey, Mike McDonell, Paul Kowalski, Jane Marie Kowalski, Ken Evans, Eleftherios P. Diamandis, K. W. Michael Siu and John Marshall

Proteomic analysis of urinary fibrinogen degradation products in patients with urothelial carcinomas

Despite many years of research efforts and continued progress in the identification of urine markers for detection of bladder cancer, none of the markers described to date has been able to replace cystoscopy a...

Authors: Pavel Gromov, Josè M. A. Moreira, Irina Gromova and Julio E. Celis

Lysate array analyses of signal transduction inhibitors in tumor cell lines

We probed the ability of reverse lysate array technology to help explain potential differences in the responses of cancer cells to various small-molecule kinase inhibitors. To understand the antitumor potentia...

Authors: Victor A. Levin, Kenji Tada and Cristian Mircean

Data mining in proteomic mass spectrometry

Data mining application to proteomic data from mass spectrometry has gained much interest in recent years. Advances made in proteomics and mass spectrometry have resulted in considerable amount of data that ca...

Authors: Asha Thomas, Georgia D. Tourassi, Adel S. Elmaghraby, Roland Valdes Jr. and Saeed A. Jortani

Proteomic and genomic technologies for biomarker discovery

Authors: Vathany Kulasingam and Eleftherios P. Diamandis

Clinical proteomics

Authors: Daniel W. Chan

Serum proteomic pattern for predicting recurrence of undifferentiated nasopharyngeal carcinoma after radiotherapy

Although most patients with early-stage nasopharyngeal carcinoma (NPC) can be cured by radiotherapy, there is a high recurrence rate in patients with advanced NPC. We attempted to identify proteomic patterns i...

Authors: Terence C. W. Poon, Shuk Man Chow, Brigette B. Y. Ma, Edwin P. Hui and Anthony T. C. Chan

In-depth analysis of the human CSF proteome using protein prefractionation

The identification of disease markers in human body fluids requires an extensive and thorough analysis of its protein constituents. In the present study, we have extended our analysis of the human cerebrospina...

Authors: Giuseppina Maccarrone, Isabel Birg, Eva Malisch, Marcus C. Rosenhagen, Claudia Ditzen, John A. Chakel, Friedrich Mandel, Andreas Reimann, Can-Carlo Doertbudak, Katrin Haegler, Florian Holsboer and Christoph W. Turck

Comparison of protein expression patterns between hepatocellular carcinoma cell lines and a hepatoblastoma cell line

Hepatocellular carcinoma (HCC) and hepatoblastoma (HB) are malignancies of the liver with different etiologies, but the HB cell line HepG2 has been frequently used in various studies of HCC. In this study, we ...

Authors: Ronald T. K. Pang, Terence C. W. Poon, Nathalie Wong, Paul B. S. Lai, Navy L. Y. Wong, Charles M. L. Chan, Jasmine W. S. Yu, Anthony T. C. Chan and Joseph J. Y. Sung

Evaluation of clinical colon carcinoma using activity-based proteomic profiling

The evaluation of clinical tumor tissues is a valuable approach to discovering novel drug targets because of the direct relevance of human samples. We used activity-based proteomic profiling (ABPP) to study th...

Authors: Melissa C. Zhang, Jiangyue Wu, Kristin G. Ardlie and Emme C. K. Lin

Antibody-based tissue profiling as a tool for clinical proteomics

Here, we show a strategy for high-throughput antibody-based tissue profiling with the aim to create an atlas of protein expression patterns in normal human tissues and cancer tissues representing the 20 most p...

Authors: Caroline Kampf, Ann-Catrin Andersson, Kenneth Wester, Erik Björling, Mathias Uhlen and Fredrik Ponten

Antiproliferative heparan sulfate inhibiting hyaluronan and transforming growth factor-β expression in human lung fibroblast cells

The objective of this study was to examine the effects of heparan sulfate (HS) on factors involved in the remodeling of connective tissue observed in patients with fibrotic respiratory disorders such as asthma...

Authors: Kristoffer Larsen, Johan Malmström, Ellen Tufvesson, György Marko-Varga and Gunilla Westergren-Thorsson

Technical evaluation of MALDI-TOF mass spectrometry for quantitative proteomic profiling matrix formulation and application

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been recently used to identify disease markers by directly profiling and quantifying the peptide/proteins in bi...

Authors: Ronald T. K. Pang, Philip J. Johnson, Charles M. L. Chan, Ebenezer K. C. Kong, Anthony T. C. Chan, Joseph J. Y. Sung and Terence C. W. Poon

The discovery of stannin in rat dorsal root ganglia using an integrated proteohistological approach

The use of proteomic analysis to discover proteins (previously identified or unknown) in a tissue sample is a valuable tool. However, there is a limit to the extent one can validate a discovery with any single...

Authors: Stanley M. Belkowski, Raymond W. Colburn, Dennis J. Stone, Christopher R. Van Besien, Deborah Polkovitch, Patricia Andrade-Gordon and Michael R. D'Andrea

New targets for an old drug

Methotrexate has been a clinical agent used in cancer, immunosuppression, rheumatoid arthritis, and other highly proliferative diseases for many years, yet its underlying molecular mechanism of action in these...

Authors: Jacek J. Slon-Usakiewicz, Andrew Pasternak, Neil Reid and Leticia M. Toledo-Sherman

Development of competitive ELISA for neosporosis by employing immunoproteomics

In this study, proteomics was used to explore the antigenic proteins that are involved in cross-reactivity during serodiagnosis between Neospora caninum (N. caninum) and Toxoplasma gondii (T. gondii). Competitive...

Authors: Yong-seung Shin, Eung-goo Lee, Gee-wook Shin, Young-rim Kim, Eun-young Lee, Jae-hoon Kim, Hwan Jang, Dae-yong Kim, Yong-hwan Kim, Gon-sup Kim, Myung-deuk Suh and Tae-sung Jung

Analysis of the human serum proteome

Changes in serum proteins that signal histopathological states, such as cancer, are useful diagnostic and prognostic biomarkers. Unfortunately, the large dynamic concentration range of proteins in serum makes ...

Authors: King C. Chan, David A. Lucas, Denise Hise, Carl F. Schaefer, Zhen Xiao, George M. Janini, Kenneth H. Buetow, Haleem J. Issaq, Timothy D. Veenstra and Thomas P. Conrads

An investigation of plasma collection, stabilization, and storage procedures for proteomic analysis of clinical samples

In order to evaluate the critical components of the process necessary to preserve clinical plasma samples collected at research sites for proteomic analysis, various collection and preservation protocols with ...

Authors: Jeffrey D. Hulmes, Deidra Bethea, Keith Ho, Shu-Pang Huang, Deborah L. Ricci, Gregory J. Opiteck and Stanley A. Hefta

Application of sector protein microarrays to clinical samples

Many protein functions are conferred by posttranslational modifications, which allow proteins to perform specific cellular tasks. Protein microarrays enable specific detection of posttranslational modification...

Authors: Virginia Espina, Emanuel F. Petricoin III, Lance A. Liotta and David Geho

Development of multiplexed protein profiling and detection using near infrared detection of reverse-phase protein microarrays

Protein microarrays have been recently employed for signal pathway profiling and high-throughput protein expression analysis. Reversephase arrays, where the array consists of immobilized analytes and lysates h...

Authors: Valerie S. Calvert, Yihui Tang, Vince Boveia, Julie Wulfkuhle, Amy Schutz-Geschwender, D. Michael Olive, Lance A. Liotta and Emanuel F. Petricoin III

Differential phosphoprofiles of EGF and EGFR kinase inhibitor-treated human tumor cells and mouse xenografts

The purpose of this phospho-proteomics study was to demonstrate the broad analysis of cellular protein phosphorylation in cells and tissue as a means to monitor changes in cellular states. As a cancer model, h...

Authors: David R. Stover, Jennifer Caldwell, Jarrod Marto, Karen Root, Juergan Mestan, Michael Stumm, Olga Ornatsky, Chris Orsi, Nina Radosevic, Linda Liao, Doriano Fabbro and Michael F. Moran

New targets for an old drug

Methotrexate has been a clinical agent used in cancer, immunosuppression, rheumatoid arthritis and other highly proliferative diseases for many years, yet its underlying molecular mechanism of action in these ...

Authors: Leticia M. Toledo-Sherman, Leroi Desouza, Christopher M. Hosfield, Linda Liao, Kelly Boutillier, Paul Taylor, Shane Climie, Linda McBroom-Cerajewski and Michael F. Moran

Unbound free fatty acid concentrations are increased in cardiac ischemia

Monitoring increased plasma unbound free fatty acid (FFA_u) concentrations has been proposed as a biomarker for myocardial ischemia. In the current study, 30 acute coronary syndrome (ACS) patients presenting in th...

Authors: Fred S. Apple, Alan M. Kleinfeld and Jesse Adams III

Skeletal muscle expression of creatine kinase-B in end-stage renal disease

The tissue specificity of creatine kinase (CK-MB) has been shown not to be absolute for the myocardium. Unexplained increases of plasma creatine kinase (CK-MB) occur in patients with skeletal muscle disease, c...

Authors: Vincent Ricchiuti, Ellen M. Voss, Arthur Ney, Mark Odland and Fred S. Apple

Clinical proteomics

Authors: Lance A. Liotta and Emanuel F. Petricoin III

Selected expression profiling of full-length proteins and their variants in human plasma

With increased interest in clinical proteomics—the comparative investigation of differential protein expression patterns for use in the diagnostic and prognostic assessment of disease states—the demand for tec...

Authors: Urban A. Kiernan, Dobrin Nedelkov, Kemmons A. Tubbs, Eric E. Niederkofler and Randall W. Nelson

Moving forward with clinical proteomics

Authors: Sam Hanash