Cancer proteomics

Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early‐stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high‐throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology. © 2012 Wiley Periodicals, Inc. Mass Spec Rev 31:583–605, 2012     

Biomarker discovery in lung cancer--promises and challenges of clinical proteomics

Lung cancer is a devastating illness with an overall poor prognosis. To effectively address this disease, early detection and novel therapeutics are required. Early detection of lung cancer is challenging, in part because of the lack of adequate tumor biomarkers. The goal of this review is to summarize the knowledge of current biomarkers in lung cancer, with a focus on important serum biomarkers. The current knowledge on the known serum cytokines and tumor biomarkers of lung cancer will be presented. Emerging trends and new findings in the search for novel diagnostic and therapeutic tumor biomarkers using proteomics technologies and platforms are emphasized, including recent advances in mass spectrometry to facilitate tumor biomarker discovery program in lung cancer. It is our hope that validation of these new research platforms and technologies will result in improved early detection, prognostication, and finally the treatment of lung cancer with potential novel molecularly targeted therapeutics.     

Mass spectrometry‐based proteomics: The road to lung cancer biomarker discovery

Lung cancer is the leading cause of cancer death in men and women in Western nations, and is among the deadliest cancers with a 5‐year survival rate of 15%. The high mortality caused by lung cancer is attributable to a late‐stage diagnosis and the lack of effective treatments. So, it is crucial to identify new biomarkers that could function not only to detect lung cancer at an early stage but also to shed light on the molecular mechanisms that underlie cancer development and serve as the basis for the development of novel therapeutic strategies. Considering that DNA‐based biomarkers for lung cancer showed inadequate sensitivity, specificity, and reproducibility, proteomics could represent a better tool for the identification of useful biomarkers and therapeutic targets for this cancer type. Among the proteomics technologies, the most powerful tool is mass spectrometry. In this review, we describe studies that use mass spectrometry‐based proteomics technologies to analyze tumor proteins and peptides, which might represent new diagnostic, prognostic, and predictive markers for lung cancer. We focus in particular on those findings that hold promise to impact significantly on the clinical management of this disease. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:129–142, 2013     

分子影像学与蛋白质组学

分子影像学与蛋白质组学都是目前最前沿、最热门的医学研究领域。分子影像学通过先进的影像技术“在体”显示与疾病相关的分子改变,而蛋白质组学通过灵敏的体外检测技术分析与疾病相关的蛋白质组变化。将分子影像技术和蛋白质组学技术结合起来,很可能相互补充、相互促进,共同推动医学诊疗技术的突破。本文将在简要介绍分子影像学和蛋白质组学各自主要特点的基础上,分析二者相互结合的价值,并展望未来发展的方向。     

Microwave-assisted proteomics

State-of-the-art proteomic analysis has recently undergone a rapid evolution; with more high-throughput analytical instrumentation and informatic tools available, sample preparation is becoming one of the rate-limiting steps in protein characterization workflows. Recently several protocols have appeared in the literature that employ microwave irradiation as a tool for the preparation of biological samples for subsequent mass spectrometric characterization. Techniques for microwave-assisted bio-catalyzed reactions (including sample reduction and alkylation, enzymatic and chemical digestion, removal and analysis of post-translational modifications and characterization of enzymes and protein-interaction sites) are described. This review summarizes the various approaches undertaken, instrumentation employed, and reduction in overall experimental time observed when microwave assistance is applied.     

Lipolytic proteomics

Activity‐based proteomics (ABP) employs small molecular probes to specifically label sets of enzymes based on their shared catalytic mechanism. Given that the vast majority of lipases belong to the family of serine hydrolases and share a nucleophilic active‐site serine as part of a catalytic triad, activity‐based probes are ideal tools to study lipases and lipolysis. Moreover, the ability of ABP to highlight or isolate specific subproteomes results in a massive decrease of sample complexity. Thereby, in‐depth analysis of enzymes of interest with mass spectrometry becomes feasible. In this review, we cover probe design, technological developments, and applications of ABP of lipases, as well as give an overview of relevant identified proteins. © 2012 Wiley Periodicals, Inc. Mass Spec Rev 31:570–582, 2012     

Subcellular proteomics

The step from the analysis of the genome to the analysis of the proteome is not just a matter of numerical complexity in terms of variants of gene products that can arise from a single gene. A significant further level of complexity is introduced by the supramolecular organization of gene products because of protein-protein interactions or targeting of proteins to specific subcellular structures. There is currently no single proteome analysis strategy that can sufficiently address all levels of the organization of the proteome. To approach an appropriate analytical complement for the interrogation of the proteome at all of the levels at which it is organized, there emerges the need for a whole arsenal of proteomics strategies. The proteome analysis at the level of subcellular structures (that can be enriched by subcellular fractionation) represents an analytical strategy that combines classic biochemical fractionation methods and tools for the comprehensive identification of proteins. Among the key potentials of this strategy is the capability to screen not only for previously unknown gene products but also to assign them, along with other known, but poorly characterized gene products, to particular subcellular structures. Furthermore, the analysis at the subcellular level is a prerequisite for the detection of important regulatory events such as protein translocation in comparative studies. This review is meant to give an overview on recent key studies in the field of proteome analysis at the level of subcellular structures, and to highlight potentials and requirements.     

Proteolytic 18O-labeling strategies for quantitative proteomics

A number of proteomic techniques have been developed to quantify proteins in biological systems. This review focuses on the quantitative proteomic technique known as "proteolytic 18O-labeling." This technique utilizes a protease and H(2)18O to produce labeled peptides, with subsequent chromatographic and mass spectrometric analysis to identify and quantify (relative) the proteins from which the peptides originated. The technique determines the ratio of individual protein's expression level between two samples relative to each other, and can be used to quantitatively examine protein expression (comparative proteomics) and post-translational modifications, and to study protein-protein interactions. The present review discusses various aspects of the 18O-labeling technique, including: its history, the advantages and disadvantages of the proteolytic 18O-labeling technique compared to other techniques, enzymatic considerations, the problem of variable incorporation of 18O atoms into peptides with a discussion on recent advancements of the technique to overcome it, computational tools to interpret the data, and a review of the biological applications.     

SiLAD:一种蛋白质组学动态分析的新技术

随着蛋白质组学的产生和发展,对蛋白质组表达水平的差异和变化进行体内的和动态的分析已势所必然地成为蛋白质组学研究的发展趋势。但是传统差异蛋白质组学方法只能提供细胞或组织内各种蛋白累积总量的信息,而不是真正意义上的蛋白质差异表达分析。 SiLAD(~(35)S in vivo Labeling Analysis for Dynamic Proteomics)技术正是基于这种需求而在本实验室创立的。SiLAD技术由于其在差异检出的灵敏度和时间分辨率方面的明显优势,以及除提供蛋白质组表达动态以外,可以提供蛋白质代谢等相关动态变化的更多信息,所以可适用于对多种生物过程进行的动态蛋白质组学研究。本文对SiLAD技术的原理及特点进行简要综述。     

Mass spectrometry-based proteomics in reproductive medicine

The emergence of powerful mass spectrometry-based proteomic techniques has added a new dimension to the field of biomedical research. Application of these high throughput methodologies in pregnancy-related pathology has contributed to the comprehension of the underlying pathophysiologies and the successful identification of relevant protein biomarkers that can potentially change early diagnosis and treatment of several medical conditions related to human pregnancy. Most of the existing research on human reproduction and gestation has focused on follicular fluid, cervical/vaginal fluid, and amniotic fluid. Although proteome technologies in reproductive medicine research are not as yet widely applied, characterization of the proteome of reproductive fluids can be expected to significantly improve maternal healthcare. This article aims to summarize the applications of mass spectrometry based technology on the most important and specific biological fluids related to reproduction and gestation.     

Cysteine tagging for MS-based proteomics

Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.     

Proteomics of brain extracellular fluid (ECF) and cerebrospinal fluid (CSF)

Mass spectrometry has become the gold standard for the identification of proteins in proteomics. In this review, I will discuss the available literature on proteomic experiments that analyze human cerebrospinal fluid (CSF) and brain extracellular fluid (ECF), mostly obtained by cerebral microdialysis. Both materials are of high diagnostic value in clinical neurology, for example, in cerebrovascular disorders like stroke, neurodegenerative diseases like Alzheimer's Disease, Parkinson's Disease, amyotrophic lateral sclerosis (ALS), traumatic brain injury and cerebral infectious and inflammatory disease, such as multiple sclerosis. Moreover, there are standard procedures for sampling. In a number of studies in recent years, biomarkers have been proposed in CSF and ECF for improved diagnosis or to control therapy, based on proteomics and mass spectrometry. I will also discuss the needs for a transition of research‐based experimental screening with mass spectrometry to fast and reliable diagnostic instrumentation for clinical use. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 29:17–28, 2010