The potentials of MS-based subproteomic approaches in medical science: the case of lysosomes and breast cancer

Because of the great number of women who are diagnosed with breast cancer each year, and though this disease presents the lowest mortality rate among cancers, breast cancer remains a major public health problem. As for any cancer, the tumorigenic and metastatic processes are still hardly understood, and the biochemical markers that allow either a precise monitoring of the disease or the classification of the numerous forms of breast cancer remain too scarce. Therefore, great hopes are put on the development of high-throughput genomic and proteomic technologies. Such comprehensive techniques should help in understanding the processes and in defining steps of the disease by depicting specific genes or protein profiles. Because techniques dedicated to the current proteomic challenges are continuously improving, the probability of the discovery of new potential protein biomarkers is rapidly increasing. In addition, the identification of such markers should be eased by lowering the sample complexity; e.g., by sample fractionation, either according to specific physico-chemical properties of the proteins, or by focusing on definite subcellular compartments. In particular, proteins of the lysosomal compartment have been shown to be prone to alterations in their localization, expression, or post-translational modifications (PTMs) during the cancer process. Some of them, such as the aspartic protease cathepsin D (CatD), have even been proven as participating actively in the disease progression. The present review aims at giving an overview of the implication of the lysosome in breast cancer, and at showing how subproteomics and the constantly refining MS-based proteomic techniques may help in making breast cancer research progress, and thus, hopefully, in improving disease treatment.     

Plant proteomics: concepts, applications, and novel strategies for data interpretation

Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.     

Power and limitations of electrophoretic separations in proteomics strategies

Proteomics can be defined as the large‐scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 28:816–843, 2009     

Applications of electron microscopy in materials science and technology (microscopy in the modern world)*

A personal overview is presented attempting to show something of the broad range of applications of techniques associated with electron microscopy in the field of materials science and technology. The importance of electron microscopy in understanding microstructure/property relationships and the evolution of microstructure is stressed. In addition, some of the important uses of electron optical techniques in the more applied areas of materials technology are surveyed. The format adopted in this presentation is to illustrate the applications of electron microscopy in materials science and technology by citing recent studies. These include investigations of deformation, of grain growth, of precipitation and phase transformations and of the determination of the structure of interfaces.     

Current mass spectrometry strategies for the analysis of pesticides and their metabolites in food and water matrices

Analysis of pesticides and their metabolites in food and water matrices continues to be an active research area closely related to food safety and environmental issues. This review discusses the most widely applied mass spectrometric (MS) approaches to pesticide residues analysis over the last few years. The main techniques for sample preparation remain solvent extraction and solid‐phase extraction. The QuEChERS (Quick, Easy, Cheap, Effective, Rugged, Safe) approach is being increasingly used for the development of multi‐class pesticide residues methods in various sample matrices. MS detectors—triple quadrupole (QqQ), ion‐trap (IT), quadrupole linear ion trap (QqLIT), time‐of‐flight (TOF), and quadrupole time‐of‐flight (QqTOF)—have been established as powerful analytical tools sharing a primary role in the detection/quantification and/or identification/confirmation of pesticides and their metabolites. Recent developments in analytical instrumentation have enabled coupling of ultra‐performance liquid chromatography (UPLC) and fast gas chromatography (GC) with MS detectors, and faster analysis for a greater number of pesticides. The newly developed “ambient‐ionization” MS techniques (e.g., desorption electrospray ionization, DESI, and direct analysis in real time, DART) hyphenated with high‐resolution MS platforms without liquid chromatography separation, and sometimes with minimum pre‐treatment, have shown potential for pesticide residue screening. The recently introduced Orbitrap mass spectrometers can provide high resolving power and mass accuracy, to tackle complex analytical problems involved in pesticide residue analysis. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:907–939, 2011     

Proteomics analysis of tumor microenvironment: Implications of metabolic and oxidative stresses in tumorigenesis

Tumorigenesis is always concomitant with microenvironmental alterations. The tumor microenvironment is a heterogeneous and complex milieu, which exerts a variety of stresses on tumor cells for proliferation, survival, or death. Recently, accumulated evidence revealed that metabolic and oxidative stresses both play significant roles in tumor development and progression that converge on a common autophagic pathway. Tumor cells display increased metabolic autonomy, and the hallmark is the exploitation of aerobic glycolysis (termed Warburg effect), which increased glucose consumption and decreased oxidative phosphorylation to support growth and proliferation. This characteristic renders cancer cells more aggressive; they devour tremendous amounts of nutrients from microenvironment to result in an ever‐growing appetite for new tumor vessel formation and the release of more “waste,” including key determinants of cell fate like lactate and reactive oxygen species (ROS). The intracellular ROS level of cancer cells can also be modulated by a variety of stimuli in the tumor microenvironment, such as pro‐growth and pro‐inflammatory factors. The intracellular redox state serves as a double‐edged sword in tumor development and progression: ROS overproduction results in cytotoxic effects and might lead to apoptotic cell death, whereas certain level of ROS can act as a second‐messenger for regulation of such cellular processes as cell survival, proliferation, and metastasis. The molecular mechanisms for cancer cell responses to metabolic and oxidative stresses are complex and are likely to involve multiple molecules or signaling pathways. In addition, the expression and modification of these proteins after metabolic or oxidative stress challenge are diverse in different cancer cells and endow them with different functions. Therefore, MS‐based high‐throughput platforms, such as proteomics, are indispensable in the global analysis of cancer cell responses to metabolic and oxidative stress. Herein, we highlight recent advances in the understanding of the metabolic and oxidative stresses associated with tumor progression with proteomics‐based systems biology approaches. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:267–311, 2013     

Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments

Proteome analysis has emerged as a powerful technology to decipher biological processes. One of the main goals is to discover biomarkers for diseases from tissues and body fluids. However, the complexity and wide dynamic range of protein expression present an enormous challenge to separation technologies and mass spectrometry (MS). In this review, we examine the limitations of proteomics, and aim towards the definition of the current key prerequisites. We focus on capillary electrophoresis coupled to mass spectrometry (CE-MS), because this technique continues to show great promise. We discuss CE-MS from an application point of view, and evaluate its merits and vices for biomarker discovery and clinical applications. Finally, we present several examples on the use of CE-MS to determine urinary biomarkers and implications for disease diagnosis, prognosis, and therapy evaluation.     

Fiber-reinforced composites in milling and grinding: machining bottlenecks and advanced strategies

Fiber-reinforced composites have become the preferred material in the fields of aviation and aerospace because of their high-strength performance in unit weight. The composite components are manufactured by near net-shape and only require finishing operations to achieve final dimensional and assembly tolerances. Milling and grinding arise as the preferred choices because of their precision processing. Nevertheless, given their laminated, anisotropic, and heterogeneous nature, these materials are considered difficult-to-machine. As undesirable results and challenging breakthroughs, the surface damage and integrity of these materials is a research hotspot with important engineering significance. This review summarizes an up-to-date progress of the damage formation mechanisms and suppression strategies in milling and grinding for the fiber-reinforced composites reported in the literature. First, the formation mechanisms of milling damage, including delamination, burr, and tear, are analyzed. Second, the grinding mechanisms, covering material removal mechanism, thermal mechanical behavior, surface integrity, and damage, are discussed. Third, suppression strategies are reviewed systematically from the aspects of advanced cutting tools and technologies, including ultrasonic vibration-assisted machining, cryogenic cooling, minimum quantity lubrication (MQL), and tool optimization design. Ultrasonic vibration shows the greatest advantage of restraining machining force, which can be reduced by approximately 60% compared with conventional machining. Cryogenic cooling is the most effective method to reduce temperature with a maximum reduction of approximately 60%. MQL shows its advantages in terms of reducing friction coefficient, force, temperature, and tool wear. Finally, research gaps and future exploration directions are prospected, giving researchers opportunity to deepen specific aspects and explore new area for achieving high precision surface machining of fiber-reinforced composites.     

Modern strategies for protein quantification in proteome analysis: advantages and limitations

Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses.     

Fluorescence microscopy: established and emerging methods, experimental strategies, and applications in immunology

Cutting-edge biophysical technologies including total internal reflection fluorescence microscopy, single molecule fluorescence, single channel opening events, fluorescence resonance energy transfer, high-speed exposures, two-photon imaging, fluorescence lifetime imaging, and other tools are becoming increasingly important in immunology as they link molecular events to cellular physiology, a key goal of modern immunology. The primary concern in all forms of microscopy is the generation of contrast; for fluorescence microscopy contrast can be thought of as the difference in intensity between the cell and background, the signal-to-noise ratio. High information-content images can be formed by enhancing the signal, suppressing the noise, or both. As improved tools, such as ICCD and EMCCD cameras, become available for fluorescence imaging in molecular and cellular immunology, it is important to optimize other aspects of the imaging system. Numerous practical strategies to enhance fluorescence microscopy experiments are reviewed. The use of instrumentation such as light traps, cameras, objectives, improved fluorescent labels, and image filtration routines applicable to low light level experiments are discussed. New methodologies providing resolution well beyond that given by the Rayleigh criterion are outlined. Ongoing and future developments in fluorescence microscopy instrumentation and technique are reviewed. This review is intended to address situations where the signal is weak, which is important for emerging techniques stressing super-resolution or live cell dynamics, but is less important for conventional applications such as indirect immunofluorescence. This review provides a broad integrative discussion of fluorescence microscopy with selected applications in immunology.     

Cascading flowlines and layout modules: Practical strategies for machine duplication in facility layouts

The standard approach for design of a layout for a high-variety low-volume (HVLV) manufacturing facility has been to use either a from-to chart or a multi-product process chart to design a process layout or a cellular layout, respectively, for the facility. Considerable research has focused on making a go-no go decision to implement any one of these two traditional layouts as the preferred layout for an HVLV manufacturing facility. This paper introduces a variety of Hybrid Cellular Layouts (HCLs) which integrate the attributes of the traditional functional, cellular and flowline layouts. The mathematical models and methods for design of two HCLs—cascading flowline layout and modular layout—are discussed in detail. Unlike the standard models in the literature, the design of the cascading flowline layout introduces a novel string-to-graph aggregation and planar graph embedding method that allows machine duplication in the layout. Similarly, the design of the Modular layout introduces a substring clustering method instead of the standard method of cluster analysis to form part families using the complete routings of the parts. For each HCL, results from an industry project are presented to demonstrate the real-world viability of the concepts, methods and software developed to support the design of HCLs for high-variety low-volume manufacturing facilities.     

Environmental and food applications of LC-tandem mass spectrometry in pesticide-residue analysis: an overview

An overview is given on pesticide-residue determination in environmental and food samples by liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS). Pesticides comprise a large number of substances that belong to many completely different chemical groups, the only common characteristic is that they are effective against pests. They still constitute a challenge in MS because there is no collective pathway for fragmentation. A brief introduction to the theory of tandem MS permits a discussion of which parameters influence the ionization efficiency when the ions are subjected to different actions. Emphasis is placed on the different tandem MS instruments: triple and ion-trap quadrupoles, and hybrid quadrupole time-of-flight (Q-TOF), including advantages and drawbacks, typical detection limits, and ion signals at low concentrations. The instrumental setup, as well as LC and mass spectrometric experimental conditions, must be carefully selected to increase the performance of the analytical system. The capacity of each instrument to provide useful data for the identification of pesticides, and the possibility to obtain structural information for the identification of target and non-target compounds, are discussed. Finally, sample preparation techniques and examples of applications are debated to reveal the potential of the current state-of-the-art technology, and to further promote the usefulness of tandem MS.     

Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics

Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.