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1.  Protein Target Quantification Decision Tree 
The utility of mass spectrometry-(MS-) based proteomic platforms and their clinical applications have become an emerging field in proteomics in recent years. Owing to its selectivity and sensitivity, MS has become a key technological platform in proteomic research. Using this platform, a large number of potential biomarker candidates for specific diseases have been reported. However, due to lack of validation, none has been approved for use in clinical settings by the Food and Drug Administration (FDA). Successful candidate verification and validation will facilitate the development of potential biomarkers, leading to better strategies for disease diagnostics, prognostics, and treatment. With the recent new developments in mass spectrometers, high sensitivity, high resolution, and high mass accuracy can be achieved. This greatly enhances the capabilities of protein biomarker validation. In this paper, we describe and discuss recent developments and applications of targeted proteomics methods for biomarker validation.
doi:10.1155/2013/701247
PMCID: PMC3562589  PMID: 23401774
2.  Biomarkers of HIV-1 associated dementia: proteomic investigation of sera 
Proteome Science  2009;7:8.
Background
New, more sensitive and specific biomarkers are needed to support other means of clinical diagnosis of neurodegenerative disorders. Proteomics technology is widely used in discovering new biomarkers. There are several difficulties with in-depth analysis of human plasma/serum, including that there is no one proteomic platform that can offer complete identification of differences in proteomic profiles. Another set of problems is associated with heterogeneity of human samples in addition intrinsic variability associated with every step of proteomic investigation. Validation is the very last step of proteomic investigation and it is very often difficult to validate potential biomarker with desired sensitivity and specificity. Even though it may be possible to validate a differentially expressed protein, it may not necessarily prove to be a valid diagnostic biomarker.
Results
In the current study we report results of proteomic analysis of sera from HIV-infected individuals with or without cognitive impairment. Application of SELDI-TOF analysis followed by weak cation exchange chromatography and 1-dimensional electrophoresis led to discovery of gelsolin and prealbumin as differentially expressed proteins which were not detected in this cohort of samples when previously investigated by 2-dimensional electrophoresis with Difference Gel Electrophoresis technology.
Conclusion
Validation using western-blot analysis led us to conclude that relative change of the levels of these proteins in one patient during a timeframe might be more informative, sensitive and specific than application of average level estimated based on an even larger cohort of patients.
doi:10.1186/1477-5956-7-8
PMCID: PMC2666658  PMID: 19292902
3.  Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges 
Clinical proteomics  2013;10(1):13.
Tremendous efforts have been made over the past few decades to discover novel cancer biomarkers for use in clinical practice. However, a striking discrepancy exists between the effort directed toward biomarker discovery and the number of markers that make it into clinical practice. One of the confounding issues in translating a novel discovery into clinical practice is that quite often the scientists working on biomarker discovery have limited knowledge of the analytical, diagnostic, and regulatory requirements for a clinical assay. This review provides an introduction to such considerations with the aim of generating more extensive discussion for study design, assay performance, and regulatory approval in the process of translating new proteomic biomarkers from discovery into cancer diagnostics. We first describe the analytical requirements for a robust clinical biomarker assay, including concepts of precision, trueness, specificity and analytical interference, and carryover. We next introduce the clinical considerations of diagnostic accuracy, receiver operating characteristic analysis, positive and negative predictive values, and clinical utility. We finish the review by describing components of the FDA approval process for protein-based biomarkers, including classification of biomarker assays as medical devices, analytical and clinical performance requirements, and the approval process workflow. While we recognize that the road from biomarker discovery, validation, and regulatory approval to the translation into the clinical setting could be long and difficult, the reward for patients, clinicians and scientists could be rather significant.
doi:10.1186/1559-0275-10-13
PMCID: PMC3850675  PMID: 24088261
Proteomic biomarker; Analytical performance; Clinical performance; Food and drug administration
4.  Plasma proteomic alterations in non-human primates and humans after chronic alcohol self-administration 
Objective diagnostics of excessive alcohol use are valuable tools in the identification and monitoring of subjects with alcohol use disorders. A number of potential biomarkers of alcohol intake have been proposed, but none have reached widespread clinical usage, often due to limited diagnostic sensitivity and specificity. In order to identify novel potential biomarkers, we performed proteomic biomarker target discovery in plasma samples from non-human primates that chronically self-administer high levels of ethanol. 2-dimensional in-gel electrophoresis (2D-DIGE) was used to quantify plasma proteins from within subject samples collected before exposure to ethanol and after three months of excessive ethanol self-administration. Highly abundant plasma proteins were depleted from plasma samples to increase proteomic coverage. Altered plasma levels of SAA4, RBP, ITIH4, clusterin, and fibronectin, identified by 2D-DIGE analysis, were confirmed in unmanipulated, whole plasma from these animals by immunoblotting. Examination of these target plasma proteins in human subjects with excessive alcohol consumption (and control subjects) revealed increased levels of SAA4 and clusterin and decreased levels of fibronectin compared to controls. These proteins not only serve as targets for further development as biomarker candidates or components of biomarker panels, but also add to the growing understanding of dysregulated immune function and lipoprotein metabolism with chronic, excessive alcohol consumption.
doi:10.1017/S1461145711000046
PMCID: PMC3107900  PMID: 21303580
Alcohol abuse; alcoholism; biomarker; diagnostic; plasma; proteomic
5.  Probing Advantages of Different Selectivity Strategies for Targeted Quantitative Proteomics 
INTRODUCTION: There has been an exponential increase in the number of ‘potential’ protein biomarkers discovered; thus requiring the need for better quantification strategies to confirm or refute their ultimate utility. Also required is increased throughput which means reduced sample preparation and/or accelerated chromatography which increases the chance of interferences that could confound robust quantification. The purpose of this study is to explore a range of new MS analysis methodologies that enable higher selectivity quantification. The different techniques rely on different properties of the molecule for specificity so their utility will depend to a large degree on the target molecules. But an exploration to determine some general guidelines will be helpful when choosing the best strategy. In this study, we compare the quantification of tryptic peptides in complex biological matrices using various strategies including combinations of sample preparation and mass spectrometric methodologies on different mass spectrometric platforms. EXPERIMENTAL METHODS: The intact or digested BNP was spiked into the crashed plasma to create calibration curves. An AB SCIEX QTRAP® 5500 system equipped with Turbo V™ source was used. Multiple reaction monitoring (MRM) transitions and MRM3 experiments for intact and digested BNP were developed and used to measure the calibration curves. For the differential mobility separations, a QTRAP 5500 system equipped with SelexION™ Technology was used. RESULTS: Three quantitative methodologies were used with the QTRAP® 5500 System: MRM provides selectivity based on the fragmentation of the peptide and monitoring of a specific product ion. When matrix interference is a problem with MRM, further selectivity can be performed using MRM3, which provides a second level of selectivity based on monitoring a secondary product ion. Alternatively, the differential mobility separation (DMS) system which provides selectivity based on the mobility of the various chemicals in the sample can also be used. Intact BNP provided good fragmentation for MS/MS and MS3, thus best sensitivity was obtained using MRM3 or MRM. However, for large peptides which do not fragment well, SIM (single ion monitoring) using DMS may be an alternative methodology for quantification.
PMCID: PMC3630610
6.  Proteomics and biomarkers in clinical trials for drug development 
Journal of proteomics  2011;74(12):2632-2641.
Proteomics allows characterization of protein structure and function, protein-protein interactions, and peptide modifications. It has given us insight into the perturbations of signaling pathways within tumor cells and has improved the discovery of new therapeutic targets and possible indicators of response to and duration of therapy. The discovery, verification, and validation of novel biomarkers are critical in streamlining clinical development of targeted compounds, and directing rational treatments for patients whose tumors are dependent upon select signaling pathways. Studies are now underway in many diseases to examine the immune or inflammatory proteome, vascular proteome, cancer or disease proteome, and other subsets of the specific pathology microenvironment. Successful assay verification and biological validation of such biomarkers will speed development of potential agents to targetable dominant pathways and lead to selection of individuals most likely to benefit. Reconsideration of analytical and clinical trials methods for acquisition, examination, and translation of proteomics data must occur before we march further into future of drug development.
doi:10.1016/j.jprot.2011.04.023
PMCID: PMC3158266  PMID: 21570499
proteomics; biomarkers; clinical trial; drug development; cancer; targeted therapy
7.  Validation Processes of Protein Biomarkers in Serum—A Cross Platform Comparison 
Sensors (Basel, Switzerland)  2012;12(9):12710-12728.
Due to insufficient biomarker validation and poor performances in diagnostic assays, the candidate biomarker verification process has to be improved. Multi-analyte immunoassays are the tool of choice for the identification and detailed validation of protein biomarkers in serum. The process of identification and validation of serum biomarkers, as well as their implementation in diagnostic routine requires an application of independent immunoassay platforms with the possibility of high-throughput. This review will focus on three main multi-analyte immunoassay platforms: planar microarrays, multiplex bead systems and, array-based surface plasmon resonance (SPR) chips. Recent developments of each platform will be discussed for application in clinical proteomics, principles, detection methods, and performance strength. The requirements for specific surface functionalization of assay platforms are continuously increasing. The reasons for this increase is the demand for highly sensitive assays, as well as the reduction of non-specific adsorption from complex samples, and with it high signal-to-noise-ratios. To achieve this, different support materials were adapted to the immobilized biomarker/ligand, allowing a high binding capacity and immobilization efficiency. In the case of immunoassays, the immobilized ligands are proteins, antibodies or peptides, which exhibit a diversity of chemical properties (acidic/alkaline; hydrophobic/hydrophilic; secondary or tertiary structure/linear). Consequently it is more challenging to develop immobilization strategies necessary to ensure a homogenous covered surface and reliable assay in comparison to DNA immobilization. New developments concerning material support for each platform are discussed especially with regard to increase the immobilization efficiency and reducing the non-specific adsorption from complex samples like serum and cell lysates.
doi:10.3390/s120912710
PMCID: PMC3478866  PMID: 23112739
clinical proteomics and diagnostic; multi-analyte immunoassays; serum screening; antibody-antigen interaction
8.  Diagnostic Proteomics: Serum Proteomic Patterns for the Detection of Early Stage Cancers 
Disease Markers  2004;19(4-5):209-218.
The ability to interrogate thousands of proteins found in complex biological samples using proteomic technologies has brought the hope of discovering novel disease-specific biomarkers. While most proteomic technologies used to discover diagnostic biomarkers are quite sophisticated, "proteomic pattern analysis" has emerged as a simple, yet potentially revolutionary, method for the early diagnosis of diseases. Utilizing this technology, hundreds of clinical samples can be analyzed per day and several preliminary studies suggest proteomic pattern analysis has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer.
doi:10.1155/2004/612071
PMCID: PMC3851082  PMID: 15258335
proteomic patterns; cancer detection; serum; mass spectrometry
9.  Proteomics in Melanoma Biomarker Discovery: Great Potential, Many Obstacles 
The present clinical staging of melanoma stratifies patients into heterogeneous groups, resulting in the application of aggressive therapies to large populations, diluting impact and increasing toxicity. To move to a new era of therapeutic decisions based on highly specific tumor profiling, the discovery and validation of new prognostic and predictive biomarkers in melanoma is critical. Genomic profiling, which is showing promise in other solid tumors, requires fresh tissue from a large number of primary tumors, and thus faces a unique challenge in melanoma. For this and other reasons, proteomics appears to be an ideal choice for the discovery of new melanoma biomarkers. Several approaches to proteomics have been utilized in the search for clinically relevant biomarkers, but to date the results have been relatively limited. This article will review the present work using both tissue and serum proteomics in the search for melanoma biomarkers, highlighting both the relative advantages and disadvantages of each approach. In addition, we review several of the major obstacles that need to be overcome in order to advance the field.
doi:10.1155/2011/181890
PMCID: PMC3195774  PMID: 22084682
10.  The Current State of Proteomics in GI Oncology 
Digestive Diseases and Sciences  2008;54(3):431-457.
Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.
doi:10.1007/s10620-008-0656-5
PMCID: PMC3045515  PMID: 19104933
Clinical proteomics; Gastrointestinal oncology; Mass spectrometry; Biomarker discovery
11.  Restructuring proteomics through verification 
Biomarkers in medicine  2010;4(6):799-803.
Proteomics technologies have revolutionized cell biology and biochemistry by providing powerful new tools to characterize complex proteomes, multiprotein complexes and post-translational modifications. Although proteomics technologies could address important problems in clinical and translational cancer research, attempts to use proteomics approaches to discover cancer biomarkers in biofluids and tissues have been largely unsuccessful and have given rise to considerable skepticism. The National Cancer Institute has taken a leading role in facilitating the translation of proteomics from research to clinical application, through its Clinical Proteomic Technologies for Cancer. This article highlights the building of a more reliable and efficient protein biomarker development pipeline that incorporates three steps: discovery, verification and qualification. In addition, we discuss the merits of multiple reaction monitoring mass spectrometry, a multiplex targeted proteomics platform, which has emerged as a potentially promising, high-throughput protein biomarker measurements technology for preclinical ‘verification’.
doi:10.2217/bmm.10.92
PMCID: PMC3041639  PMID: 21133699
biomarker; multiple reaction monitoring mass spectrometry; proteomics; verification
12.  Proteomic profiling of lymphocytes in autoimmunity, inflammation and cancer 
Lymphocytes play important roles in the balance between body defense and noxious agents involved in a number of diseases, e.g. autoimmune diseases, allergic inflammation and cancer. The proteomic analyses have been applied to identify and validate disease-associated and disease-specific biomarkers for therapeutic strategies of diseases. The proteomic profiles of lymphocytes may provide more information to understand their functions and roles in the development of diseases, although proteomic approaches in lymphocytes are still limited. The present review overviewed the proteomics-based studies on lymphocytes to headlight the proteomic profiles of lymphocytes in diseases, such as autoimmune diseases, allergic inflammation and cancer, with a special focus on lung diseases. We will explore the potential significance of diagnostic biomarkers and therapeutic targets from the current status in proteomic studies of lymphocytes and discuss the value of the currently available proteomic methodologies in the lymphocytes research.
doi:10.1186/1479-5876-12-6
PMCID: PMC3895788  PMID: 24397796
Proteomics; Lymphocyte; Autoimmune; Allergic inflammation; Cancer
13.  The application of biomarkers in clinical trials for motor neuron disease 
Biomarkers in medicine  2010;4(2):281-297.
The interest and research into disease-related biomarkers has greatly accelerated over the last 10 years. The potential clinical benefits for disease-specific biomarkers include a more rapid and accurate disease diagnosis, and potential reduction in size and duration of clinical drug trials, which would speed up drug development. The application of biomarkers into the clinical arena of motor neuron disease should both determine if a drug hits its proposed target and whether the drug alters the course of disease. This article will highlight the progress made in discovering suitable biomarker candidates from a variety of sources, including imaging, neurophysiology and proteomics. For biomarkers to have clinical utility, specific criteria must be satisfied. While there has been tremendous effort to discover biomarkers, very few have been translated to the clinic. The bottlenecks in the biomarker pipeline will be highlighted as well as lessons that can be learned from other disciplines, such as oncology.
doi:10.2217/bmm.09.71
PMCID: PMC2897051  PMID: 20406070
amyotrophic lateral sclerosis; biomarker; clinical trial; magnetic resonance; motor neuron disease; proteomics imaging
14.  Contribution of oncoproteomics to cancer biomarker discovery 
Molecular Cancer  2007;6:25.
Oncoproteomics is the study of proteins and their interactions in a cancer cell by proteomic technologies. Proteomic research first came to the fore with the introduction of two-dimensional gel electrophoresis. At the turn of the century, proteomics has been increasingly applied to cancer research with the wide-spread introduction of mass spectrometry and proteinchip. There is an intense interest in applying proteomics to foster an improved understanding of cancer pathogenesis, develop new tumor biomarkers for diagnosis, and early detection using proteomic portrait of samples. Oncoproteomics has the potential to revolutionize clinical practice, including cancer diagnosis and screening based on proteomic platforms as a complement to histopathology, individualized selection of therapeutic combinations that target the entire cancer-specific protein network, real-time assessment of therapeutic efficacy and toxicity, and rational modulation of therapy based on changes in the cancer protein network associated with prognosis and drug resistance. Besides, oncoproteomics is also applied to the discovery of new therapeutic targets and to the study of drug effects. In pace with the successful completion of the Human Genome Project, the wave of proteomics has raised the curtain on the postgenome era. The study of oncoproteomics provides mankind with a better understanding of neoplasia. In this article, the discovery of cancer biomarkers in recent years is reviewed. The challenges ahead and perspectives of oncoproteomics for biomarkers development are also addressed. With a wealth of information that can be applied to a broad spectrum of biomarker research projects, this review serves as a reference for biomarker researchers, scientists working in proteomics and bioinformatics, oncologists, pharmaceutical scientists, biochemists, biologists, and chemists.
doi:10.1186/1476-4598-6-25
PMCID: PMC1852117  PMID: 17407558
15.  Personalized medicine using DNA biomarkers: a review 
Human Genetics  2012;131(10):1627-1638.
Biomarkers are of increasing importance for personalized medicine, with applications including diagnosis, prognosis, and selection of targeted therapies. Their use is extremely diverse, ranging from pharmacodynamics to treatment monitoring. Following a concise review of terminology, we provide examples and current applications of three broad categories of biomarkers—DNA biomarkers, DNA tumor biomarkers, and other general biomarkers. We outline clinical trial phases for identifying and validating diagnostic and prognostic biomarkers. Predictive biomarkers, more generally termed companion diagnostic tests predict treatment response in terms of efficacy and/or safety. We consider suitability of clinical trial designs for predictive biomarkers, including a detailed discussion of validation study designs, with emphasis on interpretation of study results. We specifically discuss the interpretability of treatment effects if a large set of DNA biomarker profiles is available and the number of therapies is identical to the number of different profiles.
doi:10.1007/s00439-012-1188-9
PMCID: PMC3432208  PMID: 22752797
16.  Biomarkers in Acute Lung Injury – Marking Forward Progress 
Critical care clinics  2011;27(3):661-683.
In this article we review the ‘state of the art’ with regards to biomarkers for prediction, diagnosis and prognosis in acute lung injury (ALI). We begin by defining biomarkers and the goals of biomarker research in ALI including their ability to define more homogenous populations for recruitment into trials of novel therapies as well as to identify important biological pathways in the pathogenesis of ALI. Progress along four general routes is then examined. First the results of wide-ranging existing protein biomarkers are reported. Secondly, we describe newer biomarkers awaiting or with strong potential for validation. Thirdly, we report progress in the fields of genomics and proteomics. Finally given the complexity and number of potential biomarkers, we examine the results of combining clinical predictors with protein and other biomarkers to produce better prognostic and diagnostic indices.
doi:10.1016/j.ccc.2011.04.001
PMCID: PMC3134784  PMID: 21742222
biomarkers; clinical predictors; ALI; ARDS
17.  Development of reverse phase protein microarrays for the validation of clusterin, a mid-abundant blood biomarker 
Proteome Science  2009;7:15.
Background
Many putative disease blood biomarkers discovered in genomic and proteomic studies await validation in large clinically annotated cohorts of patient samples. ELISA assays require large quantities of precious blood samples and are not high-throughput. The reverse phase protein microarray platform has been developed for the high-throughput quantification of protein levels in small amounts of clinical samples.
Results
In the present study we present the development of reverse-phase protein microarrays (RPPMs) for the measurement of clusterin, a mid-abundant blood biomarker. An experimental protocol was optimized for the printing of serum and plasma on RPPMs using epoxy coated microscope slides and a non-denaturing printing buffer. Using fluorescent-tagged secondary antibodies, we achieved the reproducible detection of clusterin in spotted serum and plasma and reached a limit of detection of 780 ng/mL. Validation studies using both spiked clusterin and clinical samples showed excellent correlations with ELISA measurements of clusterin.
Conclusion
Serum and plasma spotted in the reverse phase array format allow for reliable and reproducible high-throughput validation of a mid-abundant blood biomarker such as clusterin.
doi:10.1186/1477-5956-7-15
PMCID: PMC2672067  PMID: 19348683
18.  Pancreatic Cancer Biomarkers and Their Implication in Cancer Diagnosis and Epidemiology 
Cancers  2010;2(4):1830-1837.
Pancreatic cancer is the fourth most common cause of cancer-related mortality in the United States. Biomarkers are needed to detect this cancer early during the disease development and for screening populations to identify those who are at risk. In cancer, “biomarker” refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker might be either a molecule secreted by a tumor or it can be a specific response of the body to the presence of cancer. Genetic, epigenetic, proteomic, glycomic, and imaging biomarkers can be used for cancer diagnosis, prognosis, and epidemiology. A number of potential biomarkers have been identified for pancreatic cancer. These markers can be assayed in non-invasively collected biofluids. These biomarkers need analytical and clinical validation so that they can be used for the purpose of screening and diagnosing pancreatic cancer and determining disease prognosis. In this article, the latest developments in pancreatic cancer biomarkers are discussed.
doi:10.3390/cancers2041830
PMCID: PMC3840448  PMID: 24281203
biomarker; cancer; diagnosis; epidemiology; epigenetics; glycans; methylation index; pancreas; prognosis; sensitivity; specificity; survival; treatment
19.  Update on current applications of proteomic in the study of inflammatory bowel disease 
Annals of Gastroenterology  2012;25(4):303-308.
Ulcerative colitis and Crohn’s disease are relapsing and remitting chronic disorders. So far, endoscopy is the gold standard for their diagnosis, but less invasive diagnostic biomarkers are needed. Many authors have developed techniques to individuate biomarkers such as genetic testing factor or proteins in biological samples such as serum, plasma, and cellular subpopulations. A protein fingerprint pattern, patient-unique, specific for the diagnosis of inflammatory bowel disease (IBD) and potentially able to predict the future patterns of disease and to help in diagnosis, treatment, and prognosis is of increasing interest among researchers. Nowadays, a proteomic approach may be used in the identification of major alterations of proteins in IBD, but there is still a lack in the identification of a panel of biomarkers among a significant number of patients in large clinical trials. In this review, we analyze and report the current knowledge in proteomic application and strategies in the study of IBD.
PMCID: PMC3959427
Crohn’s disease; ulcerative colitis; proteomic; biomarkers; metabolomic; nutrigenomic
20.  Statistical Methods for Proteomic Biomarker Discovery based on Feature Extraction or Functional Modeling Approaches* 
Statistics and its interface  2012;5(1):117-135.
In recent years, developments in molecular biotechnology have led to the increased promise of detecting and validating biomarkers, or molecular markers that relate to various biological or medical outcomes. Proteomics, the direct study of proteins in biological samples, plays an important role in the biomarker discovery process. These technologies produce complex, high dimensional functional and image data that present many analytical challenges that must be addressed properly for effective comparative proteomics studies that can yield potential biomarkers. Specific challenges include experimental design, preprocessing, feature extraction, and statistical analysis accounting for the inherent multiple testing issues. This paper reviews various computational aspects of comparative proteomic studies, and summarizes contributions I along with numerous collaborators have made. First, there is an overview of comparative proteomics technologies, followed by a discussion of important experimental design and preprocessing issues that must be considered before statistical analysis can be done. Next, the two key approaches to analyzing proteomics data, feature extraction and functional modeling, are described. Feature extraction involves detection and quantification of discrete features like peaks or spots that theoretically correspond to different proteins in the sample. After an overview of the feature extraction approach, specific methods for mass spectrometry (Cromwell) and 2D gel electrophoresis (Pinnacle) are described. The functional modeling approach involves modeling the proteomic data in their entirety as functions or images. A general discussion of the approach is followed by the presentation of a specific method that can be applied, wavelet-based functional mixed models, and its extensions. All methods are illustrated by application to two example proteomic data sets, one from mass spectrometry and one from 2D gel electrophoresis. While the specific methods presented are applied to two specific proteomic technologies, MALDI-TOF and 2D gel electrophoresis, these methods and the other principles discussed in the paper apply much more broadly to other expression proteomics technologies.
PMCID: PMC3693398  PMID: 23814640
Bayesian Methods; Biomarkers; Classification; False Discovery Rate; Functional Data Analysis; Functional Mixed Models; MALDI-TOF; Mass Spectrometry; Multiple Testing; Nonparametric Regression; Proteomics; Reproducibility; Robust Regression; Wavelets; 2D Gel Electrophoresis
21.  Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture 
BioMed Research International  2013;2013:783131.
Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA) were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches.
doi:10.1155/2013/783131
PMCID: PMC3613068  PMID: 23586059
22.  A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery 
PLoS ONE  2011;6(9):e24442.
Plasma is the most easily accessible source for biomarker discovery in clinical proteomics. However, identifying potential biomarkers from plasma is a challenge given the large dynamic range of proteins. The potential biomarkers in plasma are generally present at very low abundance levels and hence identification of these low abundance proteins necessitates the depletion of highly abundant proteins. Sample pre-fractionation using immuno-depletion of high abundance proteins using multi-affinity removal system (MARS) has been a popular method to deplete multiple high abundance proteins. However, depletion of these abundant proteins can result in concomitant removal of low abundant proteins. Although there are some reports suggesting the removal of non-targeted proteins, the predominant view is that number of such proteins is small. In this study, we identified proteins that are removed along with the targeted high abundant proteins. Three plasma samples were depleted using each of the three MARS (Hu-6, Hu-14 and Proteoprep 20) cartridges. The affinity bound fractions were subjected to gelC-MS using an LTQ-Orbitrap instrument. Using four database search algorithms including MassWiz (developed in house), we selected the peptides identified at <1% FDR. Peptides identified by at least two algorithms were selected for protein identification. After this rigorous bioinformatics analysis, we identified 101 proteins with high confidence. Thus, we believe that for biomarker discovery and proper quantitation of proteins, it might be better to study both bound and depleted fractions from any MARS depleted plasma sample.
doi:10.1371/journal.pone.0024442
PMCID: PMC3168506  PMID: 21931718
23.  Clinical Proteomics: Present and Future Prospects 
Clinical Biochemist Reviews  2006;27(2):99-116.
Advances in proteomics technology offer great promise in the understanding and treatment of the molecular basis of disease. The past decade of proteomics research, the study of dynamic protein expression, post-translational modifications, cellular and sub-cellular protein distribution, and protein-protein interactions, has culminated in the identification of many disease-related biomarkers and potential new drug targets. While proteomics remains the tool of choice for discovery research, new innovations in proteomic technology now offer the potential for proteomic profiling to become standard practice in the clinical laboratory. Indeed, protein profiles can serve as powerful diagnostic markers, and can predict treatment outcome in many diseases, in particular cancer. A number of technical obstacles remain before routine proteomic analysis can be achieved in the clinic; however the standardisation of methodologies and dissemination of proteomic data into publicly available databases is starting to overcome these hurdles. At present the most promising application for proteomics is in the screening of specific subsets of protein biomarkers for certain diseases, rather than large scale full protein profiling. Armed with these technologies the impending era of individualised patient-tailored therapy is imminent. This review summarises the advances in proteomics that has propelled us to this exciting age of clinical proteomics, and highlights the future work that is required for this to become a reality.
PMCID: PMC1579414  PMID: 17077880
24.  In-Depth Analysis of Human and Mouse Plasma Using 3-D and 4-D Fractionation Strategies 
In-depth profiling of plasma proteomes can potentially identify novel disease biomarkers. But few biomarkers identified by proteomic approaches have advanced to early-stage clinical testing because they often are not sufficiently disease specific. Major challenges in plasma proteome analysis include the very wide dynamic range of protein concentrations, the high protein complexity, and the substantial heterogeneity of most protein concentrations in the normal human population. Because most disease-specific biomarkers are present in blood at very low concentrations, extensive fractionation is required prior to LC-MS/MS analysis. In general, more fractionation will result in greater depth of analysis, but there is a point of diminishing return for each fractionation method and throughput decreases as the number of LC-MS/MS runs per proteome increases. A common feature of most current plasma profiling methods is to first immunodeplete as many high abundance plasma proteins as possible, followed by extensive protein fractionation of the depleted plasma prior to trypsin digestion and LC-MS/MS. In addition, reliable quantitative comparisons are needed for most types of studies. While all quantitative methods have strengths and weaknesses, label-free quantitative comparison of LC-MS signals is increasing in popularity and seems adequately reproducible for most studies. Our laboratory commonly uses two alternative plasma proteome analysis strategies. One powerful approach utilizes a 3-D protein/peptide profiling method consisting of depleting 20 abundant proteins followed by 1-D SDS PAGE, fractionation of the gel lane into 20 to 60 fractions and LC-MS/MS analysis. Proteins can be quantitatively compared using label-free analysis of ion current patterns from the MS full scans. An even greater depth of analysis can be achieved using a 4-D protein/peptide profiling strategy utilizing microscale solution isoelectrofocusing of proteins prior the SDS gel in the 3-D scheme, although throughput is substantially reduced.
PMCID: PMC3186531
25.  Discovery and identification of potential biomarkers of papillary thyroid carcinoma 
Molecular Cancer  2009;8:79.
Background
Thyroid carcinoma is the most common endocrine malignancy and a common cancer among the malignancies of head and neck. Noninvasive and convenient biomarkers for diagnosis of papillary thyroid carcinoma (PTC) as early as possible remain an urgent need. The aim of this study was to discover and identify potential protein biomarkers for PTC specifically.
Methods
Two hundred and twenty four (224) serum samples with 108 PTC and 116 controls were randomly divided into a training set and a blind testing set. Serum proteomic profiles were analyzed using SELDI-TOF-MS. Candidate biomarkers were purified by HPLC, identified by LC-MS/MS and validated using ProteinChip immunoassays.
Results
A total of 3 peaks (m/z with 9190, 6631 and 8697 Da) were screened out by support vector machine (SVM) to construct the classification model with high discriminatory power in the training set. The sensitivity and specificity of the model were 95.15% and 93.97% respectively in the blind testing set. The candidate biomarker with m/z of 9190 Da was found to be up-regulated in PTC patients, and was identified as haptoglobin alpha-1 chain. Another two candidate biomarkers (6631, 8697 Da) were found down-regulated in PTC and identified as apolipoprotein C-I and apolipoprotein C-III, respectively. In addition, the level of haptoglobin alpha-1 chain (9190 Da) progressively increased with the clinical stage I, II, III and IV, and the expression of apolipoprotein C-I and apolipoprotein C-III (6631, 8697 Da) gradually decreased in higher stages.
Conclusion
We have identified a set of biomarkers that could discriminate PTC from non-cancer controls. An efficient strategy, including SELDI-TOF-MS analysis, HPLC purification, MALDI-TOF-MS trace and LC-MS/MS identification, has been proved successful.
doi:10.1186/1476-4598-8-79
PMCID: PMC2761863  PMID: 19785722

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