Recent advances in 2D electrophoresis: an array of possibilities

Proteome profiling of Campylobacter jejuni 81-176 at 37 °C and 42 °C by label-free mass spectrometry

BACKGROUND

The main natural reservoir for Campylobacter jejuni is the avian intestinal tract. There, C. jejuni multiplies optimally at 42 °C - the avian body temperature. After infecting humans through oral intake, the bacterium encounters the lower temperature of 37 °C in the human intestinal tract. Proteome profiling by label-free mass spectrometry (DIA-MS) was performed to examine the processes which enable C. jejuni 81-176 to thrive at 37 °C in comparison to 42 °C. In total, four states were compared with each other: incubation for 12 h at 37 °C, for 24 h at 37 °C, for 12 h at 42 °C and 24 h at 42 °C.

RESULTS

It was shown that the proteomic changes not only according to the different incubation temperature but also to the length of the incubation period were evident when comparing 37 °C and 42 °C as well as 12 h and 24 h of incubation. Altogether, the expression of 957 proteins was quantifiable. 37.1 - 47.3% of the proteins analyzed showed significant differential regulation, with at least a 1.5-fold change in either direction (i.e. log2 FC ≥ 0.585 or log2 FC ≤ -0.585) and an FDR-adjusted p-value of less than 0.05. The significantly differentially expressed proteins could be arranged in 4 different clusters and 16 functional categories.

CONCLUSIONS

The C. jejuni proteome at 42 °C is better adapted to high replication rates than that at 37 °C, which was in particular indicated by the up-regulation of proteins belonging to the functional categories "replication" (e.g. Obg, ParABS, and NapL), "DNA synthesis and repair factors" (e.g. DNA-polymerase III, DnaB, and DnaE), "lipid and carbohydrate biosynthesis" (e.g. capsular biosynthesis sugar kinase, PrsA, AccA, and AccP) and "vitamin synthesis, metabolism, cofactor biosynthesis" (e.g. MobB, BioA, and ThiE). The relative up-regulation of proteins with chaperone function (GroL, DnaK, ClpB, HslU, GroS, DnaJ, DnaJ-1, and NapD) at 37 °C in comparison to 42 °C after 12 h incubation indicates a temporary lower-temperature proteomic response. Additionally the up-regulation of factors for DNA uptake (ComEA and RecA) at 37 °C compared to 42 °C indicate a higher competence for the acquisition of extraneous DNA at human body temperature.

Lipidomics and proteomics: An integrative approach for early diagnosis of dementia and Alzheimer's disease

Alzheimer's disease (AD) is the most common neurodegenerative disorder and considered to be responsible for majority of worldwide prevalent dementia cases. The number of patients suffering from dementia are estimated to increase up to 115.4 million cases worldwide in 2050. Hence, AD is contemplated to be one of the major healthcare challenge in current era. This disorder is characterized by impairment in various signaling molecules at cellular and nuclear level including aggregation of Aβ protein, tau hyper phosphorylation altered lipid metabolism, metabolites dysregulation, protein intensity alteration etc. Being heterogeneous and multifactorial in nature, the disease do not has any cure or any confirmed diagnosis before the onset of clinical manifestations. Hence, there is a requisite for early diagnosis of AD in order to downturn the progression/risk of the disorder and utilization of newer technologies developed in this field are aimed to provide an extraordinary assistance towards the same. The lipidomics and proteomics constitute large scale study of cellular lipids and proteomes in biological matrices at normal stage or any stage of a disease. The study involves high throughput quantification and detection techniques such as mass spectrometry, liquid chromatography, nuclear mass resonance spectroscopy, fluorescence spectroscopy etc. The early detection of altered levels of lipids and proteins in blood or any other biological matrices could aid in preventing the progression of AD and dementia. Therefore, the present review is designed to focus on the recent techniques and early diagnostic criteria for AD, revealing the role of lipids and proteins in this disease and their assessment through different techniques.

How to Study the Proteomes and Phosphoproteomes of Anther and Pollen

Proteomics analysis was a powerful technology for characterizing proteins and protein posttranslational modification (PTMs). Recently, many anther and pollen-related proteomic analyses have been reported, which have expanded our understanding of anther and pollen development and regulation. In this chapter, we describe a detailed, optimized protocol for the separation, digestion, tagging, and subsequent mass spectrometry-based identification and quantification of proteins and phosphoproteins from anther and pollen.

iTRAQ-based quantitative proteomic analysis of dark-germinated soybeans in response to salt stress

iTRAQ-based quantitative proteomic analysis reveals the molecular mechanisms of dark-germinated soybeans in response to salt stress.

Unraveling the Root Proteome Changes and Its Relationship to Molecular Mechanism Underlying Salt Stress Response in Radish (Raphanus sativus L.)

To understand the molecular mechanism underlying salt stress response in radish, iTRAQ-based proteomic analysis was conducted to investigate the differences in protein species abundance under different salt treatments. In total, 851, 706, and 685 differential abundance protein species (DAPS) were identified between CK vs. Na100, CK vs. Na200, and Na100 vs. Na200, respectively. Functional annotation analysis revealed that salt stress elicited complex proteomic alterations in radish roots involved in carbohydrate and energy metabolism, protein metabolism, signal transduction, transcription regulation, stress and defense and transport. Additionally, the expression levels of nine genes encoding DAPS were further verified using RT-qPCR. The integrative analysis of transcriptomic and proteomic data in conjunction with miRNAs was further performed to strengthen the understanding of radish response to salinity. The genes responsible for signal transduction, ROS scavenging and transport activities as well as several key miRNAs including miR171, miR395, and miR398 played crucial roles in salt stress response in radish. Based on these findings, a schematic genetic regulatory network of salt stress response was proposed. This study provided valuable insights into the molecular mechanism underlying salt stress response in radish roots and would facilitate developing effective strategies toward genetically engineered salt-tolerant radish and other root vegetable crops.

The impact of growth hormone on proteomic profiles: a review of mouse and adult human studies

Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies. We then examine the proteomic differences found in mice with excess circulating GH (bGH mice) or mice with disruption of the GH receptor gene (GHR^-/-). We also describe the effects of increased and decreased GH action on the proteome of adult patients with either acromegaly, GH deficiency or patients after short-term GH treatment. Finally, we explain how these proteomic studies resulted in the discovery of potential biomarkers for GH action, particularly those related with the effects of GH on aging, glucose metabolism and body composition.

Multi-gel casting apparatus for vertical polyacrylamide gels with in-built solution flow system and liquid level detectors

PAGE is the most widely used technique for the separation and biochemical analysis of biomolecules. The ever growing field of proteomics and genomics necessitates the analysis of many proteins and nucleic acid samples to understand further about the structure and function of cells. Simultaneous analysis of multiple protein samples often requires casting of many PAGE gels. Several variants of multi-gel casting/electrophoresis apparatuses are frequently used in research laboratories. Requirement of supplementary gels to match the growing demand for analyzing additional protein samples sometimes become a cause of concern. Available apparatuses are not amenable to and therefore, not recommended for any modification to accommodate additional gel casting units other than what is prescribed by the manufacturer. A novel apparatus is described here for casting multiple PAGE gels comprising four detachable components that provide enhanced practicability and performance of the apparatus. This newly modified apparatus promises to be a reliable source for making multiple gels in less time without hassle. Synchronized functioning of unique components broaden the possibilities of developing inexpensive, safe, and time-saving multi-gel casting apparatus. This apparatus can be easily fabricated and modified to accommodate desired number of gel casting units. The estimated cost (∼$300) for fabrication of the main apparatus is very competitive and effortless assembly procedure can be completed within ∼30 min.

Global Proteomic Profiling and Identification of Stress-Responsive Proteins Using Two-Dimensional Gel Electrophoresis

Global proteome profiling is a direct representation of the protein set in an organism, organ, tissues, or an organelle. One of the main objectives of proteomic analysis is the comparison and relative quantitation of proteins under a defined set of conditions. Two-dimensional gel electrophoresis (2-DE) has gained prominence over the last 4 decades for successfully aiding differential proteomics, providing visual confirmation of changes in protein abundance, which otherwise cannot be predicted from genome analysis. Each protein spot on 2-DE gel can be analyzed by its abundance, location, or even its presence or absence. This versatile gel-based method combines and utilizes the finest principle for separation of protein complexes by virtue of their charge and mass, visual mapping coupled with successful mass spectrometric identification of individual proteins.

Novel possibilities in the study of the salivary proteomic profile using SELDI-TOF/MS technology

There is currently an increasing interest in exploring human saliva to identify salivary diagnostic and prognostic biomarkers, since the collection of saliva is rapid, non-invasive and stress-free. Diagnostic tests on saliva are common and cost-effective, particularly for patients who need to monitor their hormone levels or the effectiveness of undergoing therapies. Furthermore, salivary diagnostics is ideal for surveillance studies and in situations where fast results and inexpensive technologies are required. The most important constituents of saliva are proteins, the expression levels of which may be modified due to variations of the cellular conditions. Therefore, the different profile of proteins detected in saliva, including their absence, presence or altered levels, is a potential biomarker of certain physiological and/or pathological conditions. A promising novel approach to study saliva is the global analysis of salivary proteins using proteomic techniques. In the present study, surface-enhanced laser desorption/ionization-time-of-flight/mass spectrometry (SELDI-TOF/MS), one of the most recent proteomic tools for the identification of novel biomarkers, is reviewed. In addition, the possible use of this technique in salivary proteomic studies is discussed, since SELDI technology combines the precision of matrix-assisted laser desorption/ionization-TOF/MS proteomic analysis and the high-throughput nature of protein array analysis.

Prediction of individual response to anticancer therapy: historical and future perspectives

Since the introduction of chemotherapy for cancer treatment in the early 20th century considerable efforts have been made to maximize drug efficiency and at the same time minimize side effects. As there is a great interpatient variability in response to chemotherapy, the development of predictive biomarkers is an ambitious aim for the rapidly growing research area of personalized molecular medicine. The individual prediction of response will improve treatment and thus increase survival and life quality of patients. In the past, cell cultures were used as in vitro models to predict in vivo response to chemotherapy. Several in vitro chemosensitivity assays served as tools to measure miscellaneous endpoints such as DNA damage, apoptosis and cytotoxicity or growth inhibition. Twenty years ago, the development of high-throughput technologies, e.g. cDNA microarrays enabled a more detailed analysis of drug responses. Thousands of genes were screened and expression levels were correlated to drug responses. In addition, mutation analysis became more and more important for the prediction of therapeutic success. Today, as research enters the area of -omics technologies, identification of signaling pathways is a tool to understand molecular mechanism underlying drug resistance. Combining new tissue models, e.g. 3D organoid cultures with modern technologies for biomarker discovery will offer new opportunities to identify new drug targets and in parallel predict individual responses to anticancer therapy. In this review, we present different currently used chemosensitivity assays including 2D and 3D cell culture models and several -omics approaches for the discovery of predictive biomarkers. Furthermore, we discuss the potential of these assays and biomarkers to predict the clinical outcome of individual patients and future perspectives.

Anionic branched surfactants as alternative denaturing agents for protein separations

Denaturation of a group of model proteins of diverse size and composition with three branched alkyl surfactants-sodium 2-ethylhexyl sulfate (2-EHS), sodium 3,7-dimethyloctyl sulfate (3,7-DMOS), and sodium 2-butyloctyl sulfate (2-BOS)-has been investigated using circular dichroism (CD), small-angle X-ray scattering, and polyacrylamide gel electrophoresis (PAGE). Circular dichroism reveals that 2-BOS disrupts to a higher extent the secondary structure for most of the proteins. Also, it is found that upon adsorption the shape of the protein-surfactant complexes varies from "pearl necklace" to ellipsoidal depending on the surfactant that is used. Macroscopic separations also reveal that branching sodium alkyl sulfates with n-butyl (2-BOS) and n-methyl (3,7-DMOS) groups significantly affects their performance in PAGE. 3,7-DMOS and 2-BOS result in anomalous migrations that deviate from the expected electrophoretic mobility. A combined interpretation of spectroscopy, scattering, and polyacrylamide gel electrophoresis suggests that 2-BOS promotes stronger modification of proteins during denaturation. The findings in this work aim to improve protein electrophoretic separations and the design of novel surfactants.

Microbial proteomics using mass spectrometry

Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subjects, requiring only modifications to or, in some cases, substitution of some of the steps to ensure they are relevant to the desired objective of a study. This fortunate occurrence creates an essential core of proteomic approaches and techniques that are consistently available for most studies, regardless of test subject. In this chapter, an overview of some of these core approaches, techniques, and mass spectrometric instrumentation is given, while indicating how such steps are useful for and applied to bacterial investigations. To exemplify how such proteomic concepts and techniques are applicable to bacterial investigations, a practical, quantitative method useful for bacterial proteomic analysis is presented with a discussion of possibilities, pitfalls, and some emerging technology to provide a compilation of information from the diverse literature that is intermingled with experimental experience.

Murine macrophages response to iron

Macrophages play a critical role at the crossroad between iron metabolism and immunity, being able to store and recycle iron derived from the phagocytosis of senescent erythrocytes. The way by which macrophages manage non-heme iron at physiological concentration is still not fully understood. We investigated protein changes in mouse bone marrow macrophages incubated with ferric ammonium citrate (FAC 10 μM iron). Differentially expressed spots were identified by nano RP-HPLC-ESI-MS/MS. Transcriptomic, metabolomics and western immunoblotting analyses complemented the proteomic approach. Pattern analysis was also used for identifying networks of proteins involved in iron homeostasis. FAC treatment resulted in higher abundance of several proteins including ferritins, cytoskeleton related proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) at the membrane level, vimentin, arginase, galectin-3 and macrophage migration inhibitory factor (MIF). Interestingly, GAPDH has been recently proposed to act as an alternative transferrin receptor for iron acquisition through internalization of the GAPDH-transferrin complex into the early endosomes. FAC treatment also induced the up-regulation of oxidative stress-related proteins (PRDX), which was further confirmed at the metabolic level (increase in GSSG, 8-isoprostane and pentose phosphate pathway intermediates) through mass spectrometry-based targeted metabolomics approaches. This study represents an example of the potential usefulness of "integarated omics" in the field of iron biology, especially for the elucidation of the molecular mechanisms controlling iron homeostasis in normal and disease conditions. This article is part of a Special Issue entitled: Integrated omics.

Serum proteomic signature of human chagasic patients for the identification of novel potential protein biomarkers of disease

Chagas disease is initiated upon infection by Trypanosoma cruzi. Among the health consequences is a decline in heart function, and the pathophysiological mechanisms underlying this manifestation are not well understood. To explore the possible mechanisms, we employed IgY LC10 affinity chromatography in conjunction with ProteomeLab PF2D and two-dimensional gel electrophoresis to resolve the proteome signature of high and low abundance serum proteins in chagasic patients. MALDI-TOF MS/MS analysis yielded 80 and 14 differentially expressed proteins associated with cardiomyopathy of chagasic and other etiologies, respectively. The extent of oxidative stress-induced carbonyl modifications of the differentially expressed proteins (n = 26) was increased and coupled with a depression of antioxidant proteins. Functional annotation of the top networks developed by ingenuity pathway analysis of proteome database identified dysregulation of inflammation/acute phase response signaling and lipid metabolism relevant to production of prostaglandins and arachidonic acid in chagasic patients. Overlay of the major networks identified prothrombin and plasminogen at a nodal position with connectivity to proteome signature indicative of heart disease (i.e., thrombosis, angiogenesis, vasodilatation of blood vessels or the aorta, and increased permeability of blood vessel and endothelial tubes), and inflammatory responses (e.g., platelet aggregation, complement activation, and phagocyte activation and migration). The detection of cardiac proteins (myosin light chain 2 and myosin heavy chain 11) and increased levels of vinculin and plasminogen provided a comprehensive set of biomarkers of cardiac muscle injury and development of clinical Chagas disease in human patients. These results provide an impetus for biomarker validation in large cohorts of clinically characterized chagasic patients.

Liver protein profiling in chronic hepatitis C: identification of potential predictive markers for interferon therapy outcome

The current anti-hepatitis C virus (HCV) therapy, based on pegylated-interferon alpha and ribavirin, has limited success rate and is accompanied by several side effects. The aim of this study was to identify protein profiles in pretreatment liver biopsies of HCV patients correlating with the outcome of antiviral therapy. Cytosolic or membrane/organelle-enriched protein extracts from liver biopsies of eight HCV patients were analyzed by two-dimensional fluorescence difference gel electrophoresis and mass spectrometry. Overall, this analysis identified 21 proteins whose expression levels correlate with therapy response. These factors are involved in interferon-mediated antiviral activity, stress response, and energy metabolism. Moreover, we found that post-translational modifications of dihydroxyacetone kinase were also associated with therapy outcome. Differential expression of the five best performing markers (STAT1, Mx1, DD4, DAK, and PD-ECGF) was confirmed by immunoblotting assays in an independent group of HCV patients. Finally, we showed that a prediction model based on the expression levels of these markers classifies responder and nonresponder patients with an accuracy of 85.7%. These results provide evidence that the analysis of pretreatment liver protein profiles is valuable for discriminating between responder and nonresponder HCV patients, and may contribute to reduce the number of nonresponder patients exposed to therapy-associated risks.

Proteomic analyses of host and pathogen responses during bovine mastitis

The pursuit of biomarkers for use as clinical screening tools, measures for early detection, disease monitoring, and as a means for assessing therapeutic responses has steadily evolved in human and veterinary medicine over the past two decades. Concurrently, advances in mass spectrometry have markedly expanded proteomic capabilities for biomarker discovery. While initial mass spectrometric biomarker discovery endeavors focused primarily on the detection of modulated proteins in human tissues and fluids, recent efforts have shifted to include proteomic analyses of biological samples from food animal species. Mastitis continues to garner attention in veterinary research due mainly to affiliated financial losses and food safety concerns over antimicrobial use, but also because there are only a limited number of efficacious mastitis treatment options. Accordingly, comparative proteomic analyses of bovine milk have emerged in recent years. Efforts to prevent agricultural-related food-borne illness have likewise fueled an interest in the proteomic evaluation of several prominent strains of bacteria, including common mastitis pathogens. The interest in establishing biomarkers of the host and pathogen responses during bovine mastitis stems largely from the need to better characterize mechanisms of the disease, to identify reliable biomarkers for use as measures of early detection and drug efficacy, and to uncover potentially novel targets for the development of alternative therapeutics. The following review focuses primarily on comparative proteomic analyses conducted on healthy versus mastitic bovine milk. However, a comparison of the host defense proteome of human and bovine milk and the proteomic analysis of common veterinary pathogens are likewise introduced.

The utilization of Triton X-100 for enhanced two-dimensional liquid-phase proteomics

One of the main challenges in proteomics lies in obtaining a high level of reproducible fractionation of the protein samples. Automated two-dimensional liquid phase fractionation (PF2D) system manufactured by Beckman Coulter provides a process well suited for proteome studies. However, the protein recovery efficiency of such system is low when a protocol recommended by the manufacturer is used for metaproteome profiling of environmental sample. In search of an alternative method that can overcome existing limitations, this study replaced manufacturer's buffers with Triton X-100 during the PF2D evaluation of Escherichia coli K12. Three different Triton X-100 concentrations—0.1%, 0.15%, and 0.2%—were used for the first-dimension protein profiling. As the first-dimension result was at its best in the presence of 0.15% Triton X-100, second-dimension protein fractionation was performed using 0.15% Triton X-100 and the standard buffers. When 0.15% Triton X-100 was used, protein recovery increased as much as tenfold. The elution reliability of 0.15% Triton X-100 determined with ribonuclease A, insulin, α-lactalbumin, trypsin inhibitor, and cholecystokinin (CCK) affirmed Triton X-100 at 15% can outperform the standard buffers without having adverse effects on samples. This novel use of 0.15% Triton X-100 for PF2D can lead to greater research possibilities in the field of proteomics.

Nanostructures and functional materials fabricated by interferometric lithography

Interferometric lithography (IL) is a powerful technique for the definition of large-area, nanometer-scale, periodically patterned structures. Patterns are recorded in a light-sensitive medium, such as a photoresist, that responds nonlinearly to the intensity distribution associated with the interference of two or more coherent beams of light. The photoresist patterns produced with IL are a platform for further fabrication of nanostructures and growth of functional materials and are building blocks for devices. This article provides a brief review of IL technologies and focuses on various applications for nanostructures and functional materials based on IL including directed self-assembly of colloidal nanoparticles, nanophotonics, semiconductor materials growth, and nanofluidic devices. Perspectives on future directions for IL and emerging applications in other fields are presented.

Proteomics of spermatogenesis: from protein lists to understanding the regulation of male fertility and infertility

Proteomic technologies have undergone significant development in recent years, which has led to extensive advances in protein research. Currently, proteomic approaches have been applied to many scientific areas, including basic research, various disease and malignant tumour diagnostics, biomarker discovery and other therapeutic applications. In addition, proteomics-driven research articles examining reproductive biology and medicine are becoming increasingly common. The key challenge for this field is to move from lists of identified proteins to obtaining biological information regarding protein function. The present article reviews the available scientific literature related to spermatogenesis. In addition, this study uses two-dimensional electrophoresis mass spectrometry (2DE-MS) and liquid chromatography (LC)-MS to construct a series of proteome profiles describing spermatogenesis. This large-scale identification of proteins provides a rich resource for elucidating the mechanisms underlying male fertility and infertility.

Functional proteomics to dissect tyrosine kinase signalling pathways in cancer

Advances in the generation and interpretation of proteomics data have spurred a transition from focusing on protein identification to functional analysis. Here we review recent proteomics results that have elucidated new aspects of the roles and regulation of signal transduction pathways in cancer using the epidermal growth factor receptor (EGFR), ERK and breakpoint cluster region (BCR)-ABL1 networks as examples. The emerging theme is to understand cancer signalling as networks of multiprotein machines which process information in a highly dynamic environment that is shaped by changing protein interactions and post-translational modifications (PTMs). Cancerous genetic mutations derange these protein networks in complex ways that are tractable by proteomics.

Highlights on the capacities of "Gel-based" proteomics

Gel-based proteomic is the most popular and versatile method of global protein separation and quantification. This is a mature approach to screen the protein expression at the large scale, and a cheaper approach as compared with gel-free proteomics. Based on two independent biochemical characteristics of proteins, two-dimensional electrophoresis combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass. The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis and finally protein identification by mass spectrometry. For the study of differentially expressed proteins, two-dimensional electrophoresis allows simultaneously to detect, quantify and compare up to thousand protein spots isoforms, including post-translational modifications, in the same gel and in a wide range of biological systems. In this review article, the limits, benefits, and perspectives of gel-based proteomic approaches are discussed using concrete examples.

Cross species proteomics

Proteomics has advanced in leaps and bounds over the past couple of decades. However, the continuing dependency of mass spectrometry-based protein identification on the searching of spectra against protein sequence databases limits many proteomics experiments. If there is no sequenced genome for a given species, then cross species proteomics is required, attempting to identify proteins across the species boundary, typically using the sequenced genome of a closely related species. Unlike sequence searching for homologues, the proteomics equivalent is confounded by small differences in amino acid sequences, leading to large differences in peptide masses; this renders mass matching of peptides and their product ions difficult. Therefore, the phylogenetic distance between the two species and the attendant level of conservation between the homologous proteins play a huge part in determining the extent of protein identification that is possible across the species boundary. In this chapter, we review the cross species challenge itself, as well as various approaches taken to deal with it and the success met with in past studies. This is followed by recommendations of best practice and suggestions to researchers facing this challenge as well as a final section predicting developments, which may help improve cross species proteomics in the future.

Proteomics: challenges, techniques and possibilities to overcome biological sample complexity

Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed.

Quantitative proteomic analysis of the cerebrospinal fluid of patients with multiple sclerosis

The diagnosis of multiple sclerosis (MS) is challenging for the lack of a specific diagnostic test. Recent researches in quantitative proteomics, however, offer new opportunities for biomarker discovery and the study of disease pathogenesis. To find more potential protein biomarkers, we used two technologies, 2-dimensional fluorescence difference in-gel electrophoresis (2D-DIGE), followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and ultra-performance liquid chromato-graph coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS), to quantitatively analyse differential proteomic expression in the cerebrospinal fluid (CSF) between patients with MS (the experiment group) and patients with other neurological diseases (ONDs; the control group). Analysis by the former technology identified more than 43 different protein spots (39 proteins), of which 17 spots (13 proteins) showed more than 1.5-fold difference in abundance as analysed by DeCyder software (GE Healthcare, Piscataway. NJ, USA) between the MS and the ONDs groups. The expression of five protein spots was elevated and the expression of 12 protein spots was decreased in the MS group. Meanwhile, the latter method, UPLC/Q-TOF MS showed 68 different proteins. There were 45 proteins with a difference of more than 1.5 folds between the two groups, in which the expression of 20 proteins was elevated and the expression of 25 proteins was decreased in the MS group. Data provided by the two methods indicated that the proteins overlapped ratio was 27% in the 26 significant proteins that had the same regulation tendency. The differential CSF proteins were analysed further by biological network and it revealed interaction of them. The subsequent ELISA measuring the concentration of cystatin C (P < 0.01), which was one of the proteins discovered simultaneously with the two technologies, confirmed the results of the two quantitative proteomic analysis. The combination of the two quantitative proteomic technologies was helpful in discovering differentially expressed proteins that may have a connection with MS disease physiology and serve as useful biomarkers for diagnosis and treatment of MS diseases.

High-throughput liquid-liquid fractionation of multiple protein post-translational modifications

Post-translational protein modifications have contributed significantly to the identification of macromolecular biomarkers of biological processes. We have modified a two-dimensional HPLC system (Beckman Coulter PF2D ProteomeLab) to create proteome maps of post-translational protein modifications. This system resolves complex protein mixtures by anion exchange chromatofocusing in the first dimension and hydrophobicity (reverse phase chromatography) in the second dimension. The simultaneous identification of multiple protein modifications, accomplished by incorporating a photo diode array (PDA) detector into the PF2D system, facilitates the simultaneous production of three-dimensional proteome maps and visualization of both unmodified and post-translationally modified (PTM) proteins at their signature wavelengths within the proteome. We describe procedures for the simultaneous resolution of proteome maps, the identification of proteins modified by nitration, carbonylation, and phosphorylation, and proteins with unique spectra such as the heme containing proteins.

High resolution preparation of monocyte-derived macrophages (MDM) protein fractions for clinical proteomics

BACKGROUND

Macrophages are involved in a number of key physiological processes and complex responses such as inflammatory, immunological, infectious diseases and iron homeostasis. These cells are specialised for iron storage and recycling from senescent erythrocytes so they play a central role in the fine tuning of iron balancing and distribution. The comprehension of the many physiological responses of macrophages implies the study of the related molecular events. To this regard, proteomic analysis, is one of the most powerful tools for the elucidation of the molecular mechanisms, in terms of changes in protein expression levels.

RESULTS

Our aim was to optimize a protocol for protein fractionation and high resolution mapping using human macrophages for clinical studies. We exploited a fractionation protocol based on the neutral detergent Triton X-114. The 2D maps of the fractions obtained showed high resolution and a good level of purity. Western immunoblotting and mass spectrometry (MS/MS analysis) indicated no fraction cross contamination. On 2D-PAGE mini gels (7 x 8 cm) we could count more than five hundred protein spots, substantially increasing the resolution and the number of detectable proteins for the macrophage proteome. The fractions were also evaluated, with preliminary experiments, using Surface Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS).

CONCLUSION

This relatively simple method allows deep investigation into macrophages proteomics producing discrete and accurate protein fractions, especially membrane-associated and integral proteins. The adapted protocol seems highly suitable for further studies of clinical proteomics, especially for the elucidation of the molecular mechanisms controlling iron homeostasis in normal and disease conditions.

The ongoing evolution of proteomics in malignancy

The complementary fields of genomics and proteomics offer insights into the molecular mechanisms of diseases. While genomics seeks to define our genetic substrate, proteomics explores the structure and function of proteins, which are the end effectors of our genes. Proteomics has been revolutionized in the past decade by the application of techniques such as protein arrays, two-dimensional gel electrophoresis, and mass spectrometry. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of clinical oncology. We will discuss innovations in proteomic technologies and highlight their prospective applications to patient care.

Integration of omics data: how well does it work for bacteria?

In the current omics era, innovative high-throughput technologies allow measuring temporal and conditional changes at various cellular levels. Although individual analysis of each of these omics data undoubtedly results into interesting findings, it is only by integrating them that gaining a global insight into cellular behaviour can be aimed at. A systems approach thus is predicated on data integration. However, because of the complexity of biological systems and the specificities of the data-generating technologies (noisiness, heterogeneity, etc.), integrating omics data in an attempt to reconstruct signalling networks is not trivial. Developing its methodologies constitutes a major research challenge. Besides for their intrinsic value towards health care, environment and industry, prokaryotes are ideal model systems to further develop these methods because of their lower regulatory complexity compared with eukaryotes, and the ease with which they can be manipulated. Several successful examples outlined in this review already show the potential of the systems approach for both fundamental and industrial applications, which would be time-consuming or impossible to develop solely through traditional reductionist approaches.

Applications and current challenges of proteomic approaches, focusing on two-dimensional electrophoresis

Since the formulation of the concept of "proteomics" in 1995, a plethora of proteomic technologies have been developed in order to study proteomes of tissues, cells and organelles. The powerful new technologies enabled by proteomic approaches have lead to the application of these methods to an exponentially increasing variety of biological questions for highly complex protein mixtures. Continuous technical optimization allows for an ever-increasing sensitivity of proteomic techniques. In this review, a brief overview of currently available proteomic techniques and their applications is given, followed by a more detailed description of advantages and technical challenges of two-dimensional electrophoresis (2-DE). Some solutions to circumvent currently encountered technical difficulties for 2-DE analyses are proposed.

RP-HPLC prefractionation and its application in expressional proteomics analysis of anin vitro viral infection model

Prefractionation of complex protein mixtures is an efficient method for increasing the separation power of 2-DE. RP-HPLC has been successfully utilized as a prefractionation method prior to 2-DE. Here we describe the optimization of an efficient RP-HPLC method for prefractionation of baby hamster kidney cell solubilized proteins. A step gradient elution of acetonitrile was optimized and collected fractions were further examined by SDS-PAGE and 2-DE. By utilizing this method an effective increase in separation power of 2-DE is accomplished. Moreover, we describe the application of this method to expressional proteome analysis of a virally infected cell model.

Expanding the subproteome of the inner mitochondria using protein separation technologies: one- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis

Currently no single proteomics technology has sufficient analytical power to allow for the detection of an entire proteome of an organelle, cell, or tissue. One approach that can be used to expand proteome coverage is the use of multiple separation technologies especially if there is minimal overlap in the proteins observed by the different methods. Using the inner mitochondrial membrane subproteome as a model proteome, we compared for the first time the ability of three protein separation methods (two-dimensional liquid chromatography using the ProteomeLab PF 2D Protein Fractionation System from Beckman Coulter, one-dimensional reversed phase high performance liquid chromatography, and two-dimensional gel electrophoresis) to determine the relative overlap in protein separation for these technologies. Data from these different methods indicated that a strikingly low number of proteins overlapped with less than 24% of proteins common between any two technologies and only 7% common among all three methods. Utilizing the three technologies allowed the creation of a composite database totaling 348 non-redundant proteins. 82% of these proteins had not been observed previously in proteomics studies of this subproteome, whereas 44% had not been identified in proteomics studies of intact mitochondria. Each protein separation method was found to successfully resolve a unique subset of proteins with the liquid chromatography methods being more suited for the analysis of transmembrane domain proteins and novel protein discovery. We also demonstrated that both the one- and two-dimensional LC allowed for the separation of the alpha-subunit of F1F0 ATP synthase that differed due to a change in pI or hydrophobicity.

Bioinformatics and data mining in proteomics

Proteomic studies involve the identification as well as qualitative and quantitative comparison of proteins expressed under different conditions, and elucidation of their properties and functions, usually in a large-scale, high-throughput format. The high dimensionality of data generated from these studies will require the development of improved bioinformatics tools and data-mining approaches for efficient and accurate data analysis of biological specimens from healthy and diseased individuals. Mining large proteomics data sets provides a better understanding of the complexities between the normal and abnormal cell proteome of various biological systems, including environmental hazards, infectious agents (bioterrorism) and cancers. This review will shed light on recent developments in bioinformatics and data-mining approaches, and their limitations when applied to proteomics data sets, in order to strengthen the interdependence between proteomic technologies and bioinformatics tools.

Technical innovations for the automated identification of gel-separated proteins by MALDI-TOF mass spectrometry

The combination of gel-based two-dimensional protein separations with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is the workhorse for the large-scale analyses of proteomes. Such high-throughput proteomic approaches require automation of all post-separation steps and the in-gel digest of proteins especially is often the bottleneck in the protein identification workflow. With the objective of reaching the same high performance of manual low-throughput in-gel digest procedures, we have developed a novel stack-type digestion device and implemented it into a commercially available robotic liquid handling system. This modified system is capable of performing in-gel digest, extraction of proteolytic peptides, and subsequent sample preparation for MALDI-MS without any manual intervention, but with a performance at least identical to manual procedures as indicated on the basis of the sequence coverage obtained by peptide mass fingerprinting. For further refinement of the automated protein identification workflow, we have also developed a motor-operated matrix application device to reproducibly obtain homogenous matrix preparation of high quality. This matrix preparation was found to be suitable for the automated acquisition of both peptide mass fingerprint and fragment ion spectra from the same sample spot, a prerequisite for high confidence protein identifications on the basis of peptide mass and sequence information. Due to the implementation of the stack-type digestion device and the motor-operated matrix application device, the entire platform works in a reliable, cost-effective, and sensitive manner, yielding high confidence protein identifications even for samples in the concentration range of as low as 100 fmol protein per gel plug.