Two-dimensional protein electrophoresis: From molecular pathway discovery to biomarker discovery in neurological disorders

Choe, Leila H.; Werner, Brenda G.; Lee, Kelvin H.

doi:10.1016/j.nurx.2006.05.001

Cited by 14 publications

(7 citation statements)

References 73 publications

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“…The most widely used techniques for the discovery and simultaneous profiling of multiple protein biomarkers are mass spectrometry, [16][17][18] 2-D western blotting, 19,20 2-D gel electrophoresis, 21,22 and immunological assays such as enzyme-linked immunosorbent assay (ELISA). 2,20,23 Each of these detection platforms plays an important role in the various steps involved in establishing new biomarkers; however, none of these techniques are well-suited for the comparative analysis of large numbers of samples or the multiplexed detection of many targets within an individual sample.…”

Section: Introductionmentioning

confidence: 99%

Microarray methods for protein biomarker detection

Lee

Wark

Corn

2008

Analyst

137

108

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The application of protein biomarkers as an aid for the detection and treatment of diseases has been subject to intensified interest in recent years. The quantitative assaying of protein biomarkers in easily obtainable biological fluids such as serum and urine offers the opportunity to improve patient care via earlier and more accurate diagnoses in a convenient, non-invasive manner as well as providing a potential route towards more individually targeted treatment. Essential to achieving progress in biomarker technology is the ability to screen large numbers of proteins simultaneously in a single experiment with high sensitivity and selectivity. In this article, we highlight recent progress in the use of microarrays for high-throughput biomarker profiling and discuss some of the challenges associated with these efforts. I IntroductionThe discovery of protein biomarkers whose change in expression level or state correlates with the progression of a disease is becoming increasingly important. Once validated, proposed biomarkers can be involved in achieving an earlier diagnosis, differentiating between disease types with greater accuracy, and assessing response to treatment. Prominent examples of biomarkers include proteins that are associated with a variety of cancers, 1-4 as well as heart, 5,6 renal, 7,8 andAlzheimer's 9,10 diseases.Most biomarker studies reported to date have focused on serum-, plasmaand urine-based samples. A number of other possibilities include saliva, tears, breath condensates, cerebrospinal fluid and tissue lysates extracted from biopsy samples. There are several excellent reviews detailing biomarker discovery and validation. [11][12][13][14][15] The potential benefits of biomarkers have greatly motivated both academic and industry researchers to apply new proteomic technologies for biomarker discovery and to develop quantitative analytical methodologies for rapid and sensitive biomarker detection. Many clinically relevant biomarkers reside in blood at picomolar concentrations and lower, which is five to seven orders of magnitude lower than the most abundant plasma proteins. Therefore, protein detection with high specificity and sensitivity is required; unfortunately, no universal ultrasensitive enzymatic amplification method (such as PCR for the case of nucleic acid detection) exists for proteins. Additionally, it is desirable to screen multiple proteins simultaneously in a single sample. Multiplexed measurements are attractive not only for economic reasons but also for identifying characteristic signal patterns associated with the relative changes in entire sets of proteins as this will provide much more insight and diagnostic accuracy than individual biomarker measurements.hyejinlee@knu.ac.kr. 14,19,[24][25][26][27][28][29][30] Although microarray methods are wellestablished for high-throughput nucleic acid studies, their application for protein detection has been limited by issues such as the surface immobilization of protein capture probes without loss in bioactivity as well a...

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Section: Introductionmentioning

confidence: 99%

Microarray methods for protein biomarker detection

Lee

Wark

Corn

2008

Analyst

137

108

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“…Due to this potentially high number of proteins in the secretory vesicles, they must be separated either by gel-based or liquid-based methods, before being analyzed by mass spectrometry. Traditionally, twodimensional gel electrophoresis (2D-GE) is one of the most widely used method to separate a mixture of proteins, because it separated proteins according to their isoelectric point and size (Cargile et al, 2005;Choe, Werner, & Lee, 2006). However, the main disadvantage of 2D-GE is its poor capacity to resolve membrane and hydrophobic proteins (Braun et al, 2007).…”

Section: Separation Of Secretory Vesicle Proteinsmentioning

confidence: 99%

Proteomics of regulated secretory organelles

Brunner¹,

Schvartz²,

Couté³

et al. 2009

Mass Spectrometry Reviews

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Regulated secretory organelles are important subcellular structures of living cells that allow the release in the extracellular space of crucial compounds, such as hormones and neurotransmitters. Therefore, the regulation of biogenesis, trafficking, and exocytosis of regulated secretory organelles has been intensively studied during the last 30 years. However, due to the large number of different regulated secretory organelles, only a few of them have been specifically characterized. New insights into regulated secretory organelles open crucial perspectives for a better comprehension of the mechanisms that govern cell secretion. The combination of subcellular fractionation, protein separation, and mass spectrometry is also possible to study regulated secretory organelles at the proteome level. In this review, we present different strategies used to isolate regulated secretory organelles, separate their protein content, and identify the proteins by mass spectrometry. The biological significance of regulated secretory organelles-proteomic analysis is discussed as well.

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“…In this article we will focus on a type of proteomic analysis; however, the reader is also directed to other proteomic articles in this issue. 4,5 The magnitude of the human genome and proteome is worthy of our consideration. In humans, the entire complement of protein-coding genes is now fairly solidly estimated at between 20,000 and 25,000, a surprisingly low number.…”

Section: Discovery Science In Neurodegenerative Diseasesmentioning

confidence: 99%

Liquid chromatography with tandem mass spectrometry-based proteomic discovery in aging and Alzheimer’s disease

Montine

Woltjer

Pan

et al. 2006

NeuroRX

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Summary: Systems biology offers enormous potential to understand the complexity of human brain aging and neurodegenerative diseases. Proteomics has an important role in these investigations because of its unique strengths and because of the potential central pathogenic contribution of pathological protein to several of these diseases. Here we have reviewed the methods and presented some examples of liquid chromatography-electrospray ionization-tandem mass spectrometrybased proteomics, with and without quantification using isotope-coded affinity tags, in the investigation of aging and Alzheimer's disease. As protocols and methods for improved quantitative high-throughput proteomics constantly improve, this approach will likely continue to provide deeper insight into human brain aging and neurodegenerative diseases.

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Two-dimensional protein electrophoresis: From molecular pathway discovery to biomarker discovery in neurological disorders

Cited by 14 publications

References 73 publications

Microarray methods for protein biomarker detection

Microarray methods for protein biomarker detection

Proteomics of regulated secretory organelles

Liquid chromatography with tandem mass spectrometry-based proteomic discovery in aging and Alzheimer’s disease

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