Current Proteomics
ISSN: 1570-1646
Current Proteomics
Volume 6 Number 1, April 2009
Contents
Deciphering the Antibodyome - Peptide Arrays for Serum Antibody
Biomarker Diagnostics Pp. 1-12
H. Andresen and C. Grötzinger
[Abstract] [Purchase
Issue/Articles]
Cellular Mechanisms that Edit the Immunopeptidome
Pp. 13-24
D. Georgiadou and E. Stratikos
[Abstract] [Purchase
Issue/Articles]
Affinity Purification Combined with Mass
Spectrometry-Based Proteomic Strategy to Study Mammalian Protein
Complex and Protein-Protein Interactions Pp.
25-31
S. Liang, G. Shen, X. Xu, Y. Xu and
Y. Wei
[Abstract] [Purchase
Issue/Articles]
Recent Developments in Mass Spectrometry
Analysis of Phosphoproteomes Pp. 32-42
C. Dass
[Abstract] [Purchase
Issue/Articles]
Protein Identification in Sub Proteome
Fractions of Breast Cancer Cells by OFFGEL-IEF and iTRAQ Labeling
Pp. 43-50
K.H. Chandramouli, P. Agrawal and K.N.
Thimmaiah
[Abstract] [Purchase
Issue/Articles]
Oxidation Proteomics: The Role of Thiol
Modifications Pp. 51-62
B.M. Riederer
[Abstract] [Purchase
Issue/Articles]
Proteomics on Fixed Tissue Specimens
– A Review Pp. 63-69
B.A. Reimel, S. Pan, D.H. May, S.A. Shaffer,
D.R. Goodlett, M.W. McIntosh, L.M. Yerian, M.P. Bronner, R.
Chen and T.A. Brentnall
[Abstract] [Purchase
Issue/Articles]
Abstracts
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Deciphering the Antibodyome - Peptide Arrays
for Serum Antibody Biomarker Diagnostics
H. Andresen and C. Grötzinger
The analysis of antibodies in human serum is an established
technique in the laboratory diagnosis of infectious as well
as autoimmune diseases. The multitude of antibody reactions
towards pathogens and likewise the antibody profile in autoimmune
diseases does contain a wealth of proteomic (antibody) data
that may constitute valuable diagnostic information with relevance
for the patient’s prognosis and response to therapy.
Hence the use of antibodies as diagnostic biomarkers may be
one of the most promising strategies to identify patient subgroups.
The presence or absence of antibodies directed against specific
epitopes could represent a serologic biomarker that is able
to predict the severity of a disease and assist in medical
decision making. In addition, parallel detection of many different
antibodies in a serum sample would be of great value in many
areas of basic immunological research. Peptide arrays displaying
biologically active small synthetic peptides in either low,
medium or high-density formats represent an attractive technology
to probe complex serum samples for the presence of such antibody
analytes. Holding the unique capacity to break down the heterogeneous
immunologic response into monoclonal antibody specificities
and to differentiate subtle changes in antibody abundance
and specificity, the peptide array technology by far extends
the diagnostic potential of any conventional serologic assay.
Together with an unrivalled parallelity, peptide (micro)array
analysis opens new perspectives for the novel use of antibodies
as diagnostic biomarkers and provides unique access to a more
differentiated serological diagnosis. This review recapitulates
the development of the peptide array technology with a focus
on recent advances and current state of the art platforms
for antibody diagnostics. Latest applications of peptide arrays
for the serologic diagnosis of infectious diseases, autoimmunity
and allergy are discussed, and conclusions for future developments
and implications are drawn.
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Cellular Mechanisms that Edit the Immunopeptidome
D. Georgiadou and E. Stratikos
The adaptive immune response relies on the ability of
T-lymphocytes to recognize small antigenic peptides presented
on the cell surface by specialized receptors of the Major
Histocompatibility Complex (MHC). These peptides are either
generated by the degradation of intracellular proteins (MHC
class I pathway) or by the degradation of internalized extracellular
proteins (MHC class II pathway and cross-presentation pathway).
The number of proteins that can be degraded by these pathways
runs to the thousands leading to a staggering number of possible
peptide fragments. A small subset of these peptides is selected
by the cell’s processing and presentation mechanisms
to be presented on the cell surface by MHC molecules and has
been defined as the immunopeptidome. The peptide
sequences that comprise the immunopeptidome control the immune
response and variations of this peptide repertoire are key
to understanding the host’s ability to fight pathogens,
immune response to cancer as well as predisposition to autoimmunity
and allergies. In the last few years it has been established
that the composition of the immunopeptidome is regulated by
specific cellular mechanisms that influence qualitative and
quantitative aspects of the cellular immune response in a
process that has been described as antigenic peptide editing.
This review explores the current knowledge on these cellular
mechanisms and discusses the parallels between editing the
MHC class I and class II immunopeptidomes.
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Affinity Purification Combined with Mass Spectrometry-Based
Proteomic Strategy to Study Mammalian Protein Complex and
Protein-Protein Interactions
S. Liang, G. Shen, X. Xu, Y. Xu and
Y. Wei
The versatile affinity purification techniques for isolating
mammalian protein complex in combination with mass spectrometry-based
proteomics are powerful to decipher the characters of the
associated binding partners within a protein complex and protein-protein
interactions. One single epitope-tag affinity purification
for purifying protein complex is variable and limited in protein
purity and specificity for a different individual bait protein.
Recently, several newly developed tandem affinity purification
(TAP) systems have been applied to isolate the native protein
complexes with high purity and specificity at close to physiological
levels in mammalian cells, furthermore a novel quantitative
MAP (mixing after purification)-SILAC (stable isotope labeling
with amino acids in cell culture)-based mass spectrometric
technique integrated with affinity purification effectively
investigates weak associated partners as well as deciphers
specific and dynamic protein-protein interactions.
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Recent Developments in Mass Spectrometry Analysis of Phosphoproteomes
C. Dass
Phosphorylation is one of the most important and ubiquitous
modifications in eukaryotic cells. This covalent modification
is a major signaling pathway in living beings. A vast array
of cellular events, such as proliferation, differentiation,
metabolism, signal transduction, and adaptation to environmental
stress, and the function of many proteins, hormones, neurotransmitters,
and enzymes, are triggered by phosphorylation. For understanding
highly interconnected regulatory network, it is essential
to identify and quantify phosphoproteins in biological specimens.
Currently, this task is accomplished by mass spectrometry-driven
phosphoproteomics. This article outlines recent developments
in the analysis of phosphoproteins, specifically, the enrichment,
detection, identification, and quantification of phosphopeptides/phosphoproteins.
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Protein Identification in Sub Proteome Fractions of Breast
Cancer Cells by OFFGEL-IEF and iTRAQ Labeling
K.H. Chandramouli, P. Agrawal and K.N.
Thimmaiah
To better understand the molecular mechanisms underlying
breast cancer metastasis and search for potential markers,
we applied OFFGEL-IEF, iTRAQ labeling and mass spectrometry
(LC- MS/MS) analysis to identify proteins in MDA-MB-435 breast
cancer cell line. Protein expression profiling might yield
valuable insights into molecular signals which play important
role in metastatic progression. Approximately 1250 proteins
were identified with >95%
confidence. Cathepsin D precursor, peroxiredoxin 6 (PDX6),
heat shock protein 27 (HSP27), HSP60, tropomyosin 1, annexin
I and and tumor protein D54 were identified as important cellular
proteins. Most of these proteins that were identified are
involved in cell growth, metabolism, signal transduction and
transcriptional activation. An integrated approach for mining
and visualization of iTRAQ data is presented. The results
provide an initial assessment of the proteome in MDA-MB-435
breast cancer cell line, and an improved understanding of
metastasis tumor progression.
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Oxidation Proteomics: The Role of Thiol Modifications
B.M. Riederer
Identification of thiol modifications has gained significant
importance. It is increasingly recognized that cysteines play
an important role in protein function under both physiological
and patho-physiological conditions. Here we reviewed different
approaches that are used to identify oxidized proteins and
discuss different fluorescent labeling techniques, differential
two-dimensional gel electrophoresis and matrix-assisted laser
desorption ionization – time of flight identification,
in short MALDI-TOF. We illuminate processes that depend on
protein oxidation of cysteines and we look into consequences
of thiol oxidation during aging and in a variety of diseases,
with a special reference to Alzheimer's disease. There is
an urgent need for methods that detect specifically oxidized
proteins and are able to distinguish different oxidation types.
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Proteomics on Fixed Tissue Specimens – A Review
B.A. Reimel, S. Pan, D.H. May, S.A. Shaffer,
D.R. Goodlett, M.W. McIntosh, L.M. Yerian, M.P. Bronner, R.
Chen and T.A. Brentnall
The vast majority of clinical tissue samples are formalin-fixed
and paraffin-preserved. This type of preservation has been
considered an obstacle to protein extraction from these tissues.
However, these are the very tissue samples that have associated
patient histories, diagnoses and outcomes – ideal samples
in the quest to translate bench research into clinical applications.
Thus, until recently, these valuable specimens have been unavailable
for proteomic analysis.
Over the last decade, researchers have been exploring efficient
methods to undo protein cross-linking caused by standard tissue
fixatives and extract proteins from archived tissue specimens.
These methods have been applied in different clinical proteomic
studies. In this report, we attempt to review the development
of these techniques, summarize the proteomic findings, and
discuss the impact on future clinical proteomics.
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