A review of quantitative methods for proteomic studies

Fractionation of Enriched Phosphopeptides Using pH/Acetonitrile-Gradient-Reversed-Phase Microcolumn Separation in Combination with LC-MS/MS Analysis

Mass spectrometry (MS) is a powerful and sensitive method often used for the identification of phosphoproteins. However, in phosphoproteomics, there is an identified need to compensate for the low abundance, insufficient ionization, and suppression effects of non-phosphorylated peptides. These may hamper the subsequent liquid chromatography–mass spectrometry/mass spectrometry (LC–MS/MS) analysis, resulting in incomplete phosphoproteome characterization, even when using high-resolution instruments. To overcome these drawbacks, we present here an effective microgradient chromatographic technique that yields specific fractions of enriched phosphopeptides compatible with LC–MS/MS analysis. The purpose of our study was to increase the number of identified phosphopeptides, and thus, the coverage of the sample phosphoproteome using the reproducible and straightforward fractionation method. This protocol includes a phosphopeptide enrichment step followed by the optimized microgradient fractionation of enriched phosphopeptides and final LC–MS/MS analysis of the obtained fractions. The simple fractionation system consists of a gas-tight microsyringe delivering the optimized gradient mobile phase to reversed-phase microcolumn. Our data indicate that combining the phosphopeptide enrichment with the microgradient separation is a promising technique for in-depth phosphoproteomic analysis due to moderate input material requirements and more than 3-fold enhanced protein identification.

Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies

Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.

Differential proteomic profiles and characterizations between hyalinocytes and granulocytes in ivory shell Babylonia areolata

The haemocytes of the ivory shell, Babylonia areolata are classified by morphologic observation into the following types: hyalinocytes (H) and granulocytes (G). Haemocytes comprise diverse cell types with morphological and functional heterogene and play indispensable roles in immunological homeostasis of invertebrates. In the present study, two types of haemocytes were morphologically identified and separated as H and G by Percoll density gradient centrifugation. The differentially expressed proteins were investigated between H and G using mass spectrometry. The results showed that total quantitative proteins between H and G samples were 1644, the number of up-regulated proteins in G was 215, and the number of down-regulated proteins in G was 378. Among them, cathepsin, p38 MAPK, toll-interacting protein-like and beta-adrenergic receptor kinase 2-like were up-regulated in G; alpha-2-macroglobulin-like protein, C-type lectin, galectin-2-1, galectin-3, β-1,3-glucan-binding protein, ferritin, mega-hemocyanin, mucin-17-like, mucin-5AC-like and catalytic subunit of protein kinase A were down-regulated in G. The results showed that the most significantly enriched KEGG pathways were the pathways related to ribosome, phagosome, endocytosis, carbon metabolism, protein processing in endoplasmic reticulum and oxidative phosphorylation. For phagosome and endocytosis pathway, the number of down-regulation proteins in G was more than that of up-regulation proteins. For lysosome pathway, the number of up-regulation proteins in G was more than that of down-regulation proteins. These results suggested that two sub-population haemocytes perform the different immune functions in B. areolata.

Evaluation of Gallium as a Tracer of Exogenous Hemoglobin-Haptoglobin Complexes for Targeted Drug Delivery Applications

Haptoglobin (Hp) is a plasma glycoprotein that generates significant interest in the drug delivery community because of its potential for delivery of antiretroviral medicines with high selectivity to macrophages and monocytes, the latent reservoirs of human immunodeficiency virus. As is the case with other therapies that exploit transport networks for targeted drug delivery, the success of the design and optimization of Hp-based therapies will critically depend on the ability to accurately localize and quantitate Hp-drug conjugates on the varying and unpredictable background of endogenous proteins having identical structure. In this work, we introduce a new strategy for detecting and quantitating exogenous Hp and Hp-based drugs with high sensitivity in complex biological samples using gallium as a tracer of this protein and inductively coupled plasma mass spectrometry (ICP MS) as a method of detection. Metal label is introduced by reconstituting hemoglobin (Hb) with gallium(III)-protoporphyrin IX followed by its complexation with Hp. Formation of the Hp/Hb assembly and its stability are evaluated with native electrospray ionization mass spectrometry. Both stable isotopes of Ga give rise to an abundant signal in ICP MS of a human plasma sample spiked with the metal-labeled Hp/Hb complex. The metal label signal exceeds the spectral interferences' contributions by more than an order of magnitude even with the concentration of the exogenous protein below 10 nM, the level that is more than adequate for the planned pharmacokinetic studies of Hp-based therapeutics. Graphical Abstract ᅟ.

Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli?

Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance.

BIOLOGICAL SIGNIFICANCE

This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein.

Proteomics in Traditional Chinese Medicine with an Emphasis on Alzheimer's Disease

In recent years, there has been an increasing worldwide interest in traditional Chinese medicine (TCM). This increasing demand for TCM needs to be accompanied by a deeper understanding of the mechanisms of action of TCM-based therapy. However, TCM is often described as a concept of Chinese philosophy, which is incomprehensible for Western medical society, thereby creating a gap between TCM and Western medicine (WM). In order to meet this challenge, TCM research has applied proteomics technologies for exploring the mechanisms of action of TCM treatment. Proteomics enables TCM researchers to oversee various pathways that are affected by treatment, as well as the dynamics of their interactions with one another. This review discusses the utility of comparative proteomics to better understand how TCM treatment may be used as a complementary therapy for Alzheimer's disease (AD). Additionally, we review the data from comparative AD-related TCM proteomics studies and establish the relevance of the data with available AD hypotheses, most notably regarding the ubiquitin proteasome system (UPS).

Novel biological activity of ameloblastin in enamel matrix derivative

OBJECTIVE

Enamel matrix derivative (EMD) is used clinically to promote periodontal tissue regeneration. However, the effects of EMD on gingival epithelial cells during regeneration of periodontal tissues are unclear. In this in vitro study, we purified ameloblastin from EMD and investigated its biological effects on epithelial cells.

MATERIAL AND METHODS

Bioactive fractions were purified from EMD by reversed-phase high-performance liquid chromatography using hydrophobic support with a C18 column. The mouse gingival epithelial cell line GE-1 and human oral squamous cell carcinoma line SCC-25 were treated with purified EMD fraction, and cell survival was assessed with a WST-1 assay. To identify the proteins in bioactive fractions of EMD, we used proteome analysis with two-dimensional gel electrophoresis followed by identification with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis.

RESULTS

Purified fractions from EMD suppressed proliferation of GE-1 and SCC-25. LC-MS/MS revealed that ameloblastin in EMD is the component responsible for inhibiting epithelial cell proliferation. The inhibitory effect of ameloblastin on the proliferation of GE-1 and SCC-25 was confirmed using recombinant protein.

CONCLUSION

The inhibitory effects of EMD on epithelial cell proliferation are caused by the biological activities of ameloblastin, which suggests that ameloblastin is involved in regulating epithelial downgrowth in periodontal tissues.

Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.)

Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC-MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30% of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.

Proteomics meets blue biotechnology: a wealth of novelties and opportunities

Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry.

2DE analysis of forest tree proteins using fluorescent labels and multiplexing

Although proteomists working with gel-free methods are considering the gels as coming from the past, proteomics based on gels has still a lot of opportunities to offer and acquisition of images on which thousands of spots may be resolved is still largely performed. Nowadays, two-dimensional electrophoresis remains a powerful tool to explore the plant proteome and to unravel changes in protein abundance between samples. Some weak points can be pointed out, as for any method, as for example the lack of reproducibility, or the detection of low-abundance proteins. The use of the technique called "difference gel electrophoresis" or "DIGE" can help to overcome or at least to reduce these inconveniences. DIGE requires the labelling of proteins by fluorochromes prior to their separation on 2DE gels. This technique may be applied to a wide array of plant stress studies, among others to trees. Accurate quantitative results can then be obtained and proteins presenting an interest in the studied stress are subsequently subjected to an enzymatic digestion (usually with trypsin) and identified using electrospray ionization, matrix-assisted laser desorption/ionization-time-of-flight-MS, and/or tandem MS.

Nonlabeled quantitative proteomic comparison identifies differences in acid resistance between Escherichia coli O157:H7 curli production variants

To understand the nature of a bacterial strain, it is necessary to be able to identify and measure the proteins expressed by the bacteria. In this research, the entire protein complements produced by Escherichia coli O157:H7 strain 43894OW and its naturally occurring curli producing variant 43894OR were compared to better understand the unique capabilities of these two closely related strains. A nonlabeled proteomic comparison was performed utilizing the spectra counting and peptide fractionation abilities of a quadrupole-time of flight analyzer mass spectrometer to identify and quantitate the proteins produced by the two strains. The process reliably identified and measured the concentration of 419 proteins from strains 43894OW and 43894OR within three separate biological replicates. From these two sets, 59 proteins were identified that were preferentially expressed in strain 43894OW compared to 43894OR and 14 proteins that were conversely preferentially expressed in 43894OR. A subset of the preferentially expressed proteins was assayed to determine whether their levels of gene transcription corresponded with the observed protein expression. From the resulting list of confirmed differentially expressed proteins, it was observed that the proteins contributing to acid survival--GadA and GadB--were overexpressed in 43894OW compared to 43894OR. The predicted enhanced acid resistance phenotype of 43894OW was confirmed by experimentation at pH 2.5. Additionally, a knockout mutation in the csgD genes of the 43894OR strain was constructed and suggested that CsgD had a repressive effect on acid survival in 43894OR.

Quantitative phosphoproteomics using acetone-based peptide labeling: method evaluation and application to a cardiac ischemia/reperfusion model

Mass spectrometry (MS) techniques to globally profile protein phosphorylation in cellular systems that are relevant to physiological or pathological changes have been of significant interest in biological research. An MS-based strategy utilizing an inexpensive acetone-based peptide-labeling technique known as reductive alkylation by acetone (RABA) for quantitative phosphoproteomics was explored to evaluate its capacity. Because the chemistry for RABA labeling for phosphorylation profiling had not been previously reported, it was first validated using a standard phosphoprotein and identical phosphoproteomes from cardiac tissue extracts. A workflow was then utilized to compare cardiac tissue phosphoproteomes from mouse hearts not expressing FGF2 versus hearts expressing low-molecular-weight fibroblast growth factor-2 (LMW FGF2) to relate low-molecular-weight fibroblast growth factor-2 (LMW FGF2)-mediated cardioprotective phenomena induced by ischemia/reperfusion injury of hearts, with downstream phosphorylation changes in LMW FGF2 signaling cascades. Statistically significant phosphorylation changes were identified at 14 different sites on 10 distinct proteins, including some with mechanisms already established for LMW FGF2-mediated cardioprotective signaling (e.g., connexin-43), some with new details linking LMW FGF2 to the cardioprotective mechanisms (e.g., cardiac myosin binding protein C or cMyBPC), and also several new downstream effectors not previously recognized for cardio-protective signaling by LMW FGF2. Additionally, one of the phosphopeptides, cMyBPC/pSer-282, identified was further verified with site-specific quantification using an SRM (selected reaction monitoring)-based approach that also relies on isotope labeling of a synthetic phosphopeptide with deuterated acetone as an internal standard. Overall, this study confirms that the inexpensive acetone-based peptide labeling can be used in both exploratory and targeted quantification phosphoproteomic studies to identify and verify biologically relevant phosphorylation changes in whole tissues.

Emerging mass spectrometry-based approaches to probe protein-receptor interactions: focus on overcoming physiological barriers

Physiological barriers, such as the blood-brain barrier and intestinal epithelial barrier, remain significant obstacles towards wider utilization of biopharmaceutical products. Receptor-mediated transcytosis has long been viewed as an attractive means of crossing such barriers, but successful exploitation of this route requires better understanding of the interactions between the receptors and protein-based therapeutics. Detailed characterization of such processes at the molecular level is challenging due to the very large physical size and heterogeneity of these species, which makes use of many state-of-the art analytical techniques, such as high-resolution NMR and X-ray crystallography impractical. Mass spectrometry has emerged in the past decade as a powerful tool to study protein-receptor interactions, although its applications to investigate interaction of biopharmaceuticals with their physiological partners are still limited. We highlight the potential of this technique by considering several recent examples where it had been instrumental for understanding molecular mechanisms critical for receptor-mediated transcytosis of transferrin-based therapeutics.

Proteomics applied to transfusion plasma: the beginning of the story

'Safe blood' is and has always been the major concern in transfusion medicine. Plasma can undergo virus inactivation treatments based on physicochemical, photochemical or thermal methodologies for pathogen inactivation. The validation of these treatments is essentially based on clottability assays and clotting factors' titration; however, their impact on plasma proteins at the molecular level has not yet been evaluated. Proteomics appears as particularly adapted to identify, to localize and, consequently, to correlate these modifications to the biological activity change. At the crossroads of biology and analytical sciences, proteomics is the large-scale study of proteins in tissues, physiological fluids or cells at a given moment and in a precise environment. The proteomic strategy is based on a set of methodologies involving separative techniques like mono- and bidimensional gel electrophoresis and chromatography, analytical techniques, especially mass spectrometry, and bioinformatics. Even if plasma has been extensively studied since the very beginning of proteomics, its application to transfusion medicine has just begun. In the first part of this review, we present the principles of proteomics analysis. Then, we propose a state of the art of proteomics applied to plasma analysis. Finally, the use of proteomics for the evaluation of the impact of storage conditions and pathogen inactivation treatments applied to transfusion plasma and for the evaluation of therapeutic protein fractionated is discussed.

Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening

Due to increasingly available bacterial genomes in databases, proteomic tools have recently been used to screen proteins expressed by micro-organisms in food in order to better understand their metabolism in situ. While the main objective is the systematic identification of proteins, the next step will be to bridge the gap between identification and quantification of these proteins. For that purpose, a new mass spectrometry-based approach was applied, using isobaric tagging reagent for quantitative proteomic analysis (iTRAQ), which are amine specific and yield labelled peptides identical in mass. Experimental Swiss-type cheeses were manufactured from microfiltered milk using Streptococcus thermophilus ITG ST20 and Lactobacillus helveticus ITG LH1 as lactic acid starters. At three ripening times (7, 20 and 69 days), cheese aqueous phases were extracted and enriched in bacterial proteins by fractionation. Each sample, standardised in protein amount prior to proteomic analyses, was: i) analysed by 2D-electrophoresis for qualitative analysis and ii) submitted to trypsinolysis, and labelled with specific iTRAQ tag, one per ripening time. The three labelled samples were mixed together and analysed by nano-LC coupled on-line with ESI-QTOF mass spectrometer. Thirty proteins, both from bacterial or bovine origin, were identified and efficiently quantified. The free bacterial proteins detected were enzymes from the central carbon metabolism as well as stress proteins. Depending on the protein considered, the quantity of these proteins in the cheese aqueous extract increased from 2.5 to 20 fold in concentration from day 7 to day 69 of ripening.

Advances and challenges in analytical characterization of biotechnology products: mass spectrometry-based approaches to study properties and behavior of protein therapeutics

Biopharmaceuticals are a unique class of medicines due to their extreme structural complexity. The structure of these therapeutic proteins is critically important for their efficacy and safety, and the ability to characterize it at various levels (from sequence to conformation) is critical not only at the quality control stage, but also throughout the discovery and design stages. Biological mass spectrometry (MS) offers a variety of approaches to study structure and behavior of complex protein drugs and has already become a default tool for characterizing the covalent structure of protein therapeutics, including sequence and post-translational modifications. Recently, MS-based methods have also begun enjoying a dramatic growth in popularity as a means to provide information on higher order structure and dynamics of biotechnology products. In particular, hydrogen/deuterium exchange MS and charge state distribution analysis of protein ions in electrospray ionization (ESI) MS offer a convenient way to assess the integrity of protein conformation. Native ESI MS also allows the interactions of protein drugs with their therapeutic targets and other physiological partners to be monitored using simple model systems. MS-based methods are also applied to study pharmacokinetics of biopharmaceutical products, where they begin to rival traditional immunoassays. MS already provides valuable support to all stages of development of biopharmaceuticals, from discovery to post-approval monitoring, and its impact on the field of biopharmaceutical analysis will undoubtedly continue to grow.

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.

Pitfalls in protein quantitation using acid-catalyzed O18 labeling: hydrolysis-driven deamidation

Proteolysis combined with O(18) labeling emerged recently as a powerful tool for quantitation of proteins for which suitable internal standards cannot be produced using molecular biology methods. Several recent reports suggested that acid-catalyzed O(18) labeling may be superior to the commonly accepted enzymatic protocol, as it may allow more significant spacing between the isotopic clusters of labeled and unlabeled peptides, thereby eliminating signal interference and enhancing the quality of quantitation. However, careful examination of this procedure reveals that the results of protein quantitation assisted by acid-catalyzed O(18) labeling are highly peptide-dependent. The inconsistency was found to be caused by deamidation of Asn, Gln, and carbamidomethylated Cys residues during prolonged exposure of the proteolytic fragments to the acidic environment of the labeling reaction, which translates into a loss in signal for these peptides. Taking deamidation into account leads to a significant improvement in the consistency of quantitation across a range of different proteolytic fragments.

Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information

Background

Amino acid assimilation is crucial for bacteria and this is particularly true for Lactic Acid Bacteria (LAB) that are generally auxotroph for amino acids. The global response of the LAB model Lactococcus lactis ssp. lactis was characterized during progressive isoleucine starvation in batch culture using a chemically defined medium in which isoleucine concentration was fixed so as to become the sole limiting nutriment. Dynamic analyses were performed using transcriptomic and proteomic approaches and the results were analysed conjointly with fermentation kinetic data.

Results

The response was first deduced from transcriptomic analysis and corroborated by proteomic results. It occurred progressively and could be divided into three major mechanisms: (i) a global down-regulation of processes linked to bacterial growth and catabolism (transcription, translation, carbon metabolism and transport, pyrimidine and fatty acid metabolism), (ii) a specific positive response related to the limiting nutrient (activation of pathways of carbon or nitrogen metabolism and leading to isoleucine supply) and (iii) an unexpected oxidative stress response (positive regulation of aerobic metabolism, electron transport, thioredoxin metabolism and pyruvate dehydrogenase). The involvement of various regulatory mechanisms during this adaptation was analysed on the basis of transcriptomic data comparisons. The global regulator CodY seemed specifically dedicated to the regulation of isoleucine supply. Other regulations were massively related to growth rate and stringent response.

Conclusion

This integrative biology approach provided an overview of the metabolic pathways involved during isoleucine starvation and their regulations. It has extended significantly the physiological understanding of the metabolism of L. lactis ssp. lactis. The approach can be generalised to other conditions and will contribute significantly to the identification of the biological processes involved in complex regulatory networks of micro-organisms.

Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane

Gluconacetobacter diazotrophicus is a plant-growth-promoting bacterium that colonizes sugarcane. In order to investigate molecular aspects of the G. diazotrophicus-sugarcane interaction, we performed a quantitative mass spectrometry-based proteomic analysis by (15)N metabolic labeling of bacteria, root samples, and co-cultures. Overall, more than 400 proteins were analyzed and 78 were differentially expressed between the plant-bacterium interaction model and control cultures. A comparative analysis of the G. diazotrophicus in interaction with two distinct genotypes of sugarcane, SP70-1143 and Chunee, revealed proteins with fundamental roles in cellular recognition. G. diazotrophicus presented proteins involved in adaptation to atypical conditions and signaling systems during the interaction with both genotypes. However, SP70-1143 and Chunee, sugarcane genotypes with high and low contribution of biological nitrogen fixation, showed divergent responses in contact with G. diazotrophicus. The SP70-1143 genotype overexpressed proteins from signaling cascades and one from a lipid metabolism pathway, whereas Chunee differentially synthesized proteins involved in chromatin remodeling and protein degradation pathways. In addition, we have identified 30 bacterial proteins in the roots of the plant samples; from those, nine were specifically induced by plant signals. This is the first quantitative proteomic analysis of a bacterium-plant interaction, which generated insights into early signaling of the G. diazotrophicus-sugarcane interaction.

Data management in mass spectrometry-based proteomics

Mass spectrometry-based proteomics has made the transition from the analysis of a single or only a few proteins per experiment to a high-throughput platform for discovery/validation that can analyze several hundreds to thousands of proteins in a single experiment. This increase in analytical capability hinged on four main components: (1) innovative methodologies, (2) improved instruments, (3) ready availability of comprehensive protein sequence databases, and (4) development of sophisticated software algorithms to match fragmentation mass spectra against these databases. But as the throughput of the approach increased, so did the necessity to manage and automate the data processing workflow. Indeed, modern instruments generate tens of thousands of fragmentation spectra per hour, providing a substantial bioinformatics challenge. This chapter provides insight into the specifics of this challenge, by looking at a typical workflow, the data types and user roles involved, and a broad overview of available software solutions. Finally, the increasingly important link between a local data management system and the global, centralized dissemination of proteomics data is discussed.

Bioinformatics challenges in mass spectrometry-driven proteomics

Mass spectrometry-based proteomics has become an essential part of the analytical toolbox of the life sciences. With the ability to identify and quantify hundreds to thousands of proteins in high throughput, the field has contributed its fair share to the data avalanche coming from the so-called omics fields. As a result, the challenges involved in processing and managing this flood of data have grown as well. This chapter will point out and discuss these challenges, starting from the processing of raw mass spectrometry data into peaks, over the identification of peptides and proteins, to the quantification of the identified molecules. Finally, the informatics aspects of the nascent field of targeted proteomics are outlined as well.

Proteomic identification of proteinase inhibitors in the porcine enamel matrix derivative, EMD(®)

BACKGROUND AND OBJECTIVE

The porcine enamel matrix derivative, EMD(®), which is the active component of Emdogain(®), is used widely in periodontics because of its ability to promote the regeneration of soft and hard tissues and to reduce inflammation. Previous studies have used indirect methods to explain its angiogenic and proliferative effects on cells associated with wound healing. In this study we used proteomic techniques to identify proteins in EMD other than amelogenins.

MATERIAL AND METHODS

Proteins in EMD were separated by two-dimensional gel electrophoresis and were identified using mass spectrometry. Proteomic results were validated by western blot analysis of Emdogain.

RESULTS

Fourteen proteins of porcine origin were identified and included the serine and cysteine proteinase inhibitors alpha1-antichymotrypsin and fetuin A, respectively. Alpha1-antichymotrypsin is an acute-phase factor that has been reported to indirectly down-regulate the expression of the gelatinase MMP-9. Fetuin A, a major glycoprotein component of bone and teeth, is a potent inhibitor of ectopic calcification of vascular and soft tissues and has been implicated in both osteogenesis and bone resorption. It also facilitates plasma membrane repair in damaged fibroblasts.

CONCLUSION

EMD contains a number of high-molecular-weight compounds which include the proteinase inhibitors, fetuin A and alpha1-antichymotrypsin.

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.

Proteomics and islet research

The complementary disciplines of genomics and proteomics offer better insights into the molecular mechanisms of diseases. While genomics hunts for defining our static genetic substrate, proteomics explores the structure and function of proteins expressed by a cell or tissue type under specified conditions. In the past decade, proteomics has been revolutionized by the application of techniques such as two-dimensional gel electrophoresis (2DGE), mass spectrometry (MS), and protein arrays. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of islet and diabetes research. This chapter will highlight the contributions of proteomic technologies toward the dissection of complex network of signaling molecules regulating islet function, the identification of potential biomarkers, and the understanding of mechanisms involved in the pathogenesis of diabetes.

Fast proteomic protocol for biomarker fingerprinting in cancerous cells

The advance of novel technologies that will enable the detection of large sets of biomarker proteins, to greatly improve the sensitivity and specificity of an assay, represents a major objective in biomedical research. To demonstrate the power of mass spectrometry (MS) detection for large-scale biomarker screening in cancer research, a simple, one-step approach for fast biomarker fingerprinting in complex cellular extracts is described. MCF-7 breast cancer cells were used as a model system. Fast proteomic profiling of whole cellular extracts was achieved on a linear trap quadrupole (LTQ) mass spectrometer by one of the following techniques: (a) data-dependent liquid chromatography (LC)-MS/MS of un-labeled cell extracts, (b) data-dependent LC-MS/MS with pulsed Q dissociation (PQD) detection of iTRAQ labeled samples, and (c) multiple reaction monitoring (MRM)-MS of low abundant proteins that could not be detected with data-dependent MS/MS. The data-dependent LC-MS/MS analysis of MCF-7 cells enabled the identification of 796 proteins (p<0.001) and the simultaneous detection of 156 previously reported putative cancer biomarkers. PQD detection of iTRAQ labeled cells resulted in the detection of 389 proteins and 64 putative biomarkers. MRM-MS analysis enabled the successful monitoring of a panel of low-abundance proteins in one single experiment, highlighting the utility of this technique for targeted analysis in cancer investigations. These results demonstrate that MS-based technologies relying on a one-step separation protocol have the potential to revolutionize biomarker research and screening applications by enabling fast, sensitive and reliable detection of large panels of putative biomarkers. To further stimulate the exploration of proteins that have been previously reported in the literature to be differentially expressed in a variety of cancers, an extensive list of approximately 1100 candidate biomarkers has been compiled and included in the manuscript.

Mass spectrometry analysis of C-terminal posttranslational modifications of tubulins

In mammalian brain and ciliary axonemes from ciliates, alpha- and beta-tubulins exhibit an extraordinary heterogeneity due to a combination of multigene family expression and numerous posttranslational modifications (PTMs). The combination of several PTMs located in the C-terminal tail of tubulins plays a major role in this important polymorphism of tubulin: polyglutamylation, polyglycylation, detyrosination, tyrosination, removal of the penultimate glutamate residue, and phosphorylation. In order to document the relationship and functions of these PTMs, we have developed a tubulin C-terminal Peptide Mass Fingerprinting (PMF) method. Using simplified microtubule proteins and tubulin C-terminal peptides purifications, direct matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) analysis can generate a complete picture of all tubulin isotype-specific C-terminal peptides together with their respective PTMs. This chapter will illustrate the capability of this approach to compare tubulin isoform compositions and document the changes in PTMs between samples with different tubulin assembly properties or consecutively to inactivation of modification sites or modification enzymes. Complementary MS-based approaches useful to document the structure of the highly heterogeneous posttranslational polymodifications will also be presented.

Difference gel electrophoresis as a tool to discover stress-regulated proteins

Two-dimensional electrophoresis is a powerful tool to explore the plant proteome and to unravel changes in protein expression between samples. However, the acquisition of images on which thousands of spots may be resolved has some weak points, as always pointed out by scientists working with gel-free techniques, such as the lack of reproducibility. Nowadays, this inconvenience can be bypassed by the use of a technique known as "difference gel electrophoresis" or DIGE. This technique requires the labelling of proteins by fluorochromes before their separation on 2DE gels. This technique may be applied to a wide array of plant stress studies. Providing accurate quantitative results, differentially abundant spots are usually subjected to tryptic digestion and identified using electrospray ionization, matrix-assisted laser desorption/ionization-time of flight-MS and/or tandem MS.

Comparative high-speed profiling of carboxylic acid metabolite levels by differential isotope-coded MALDI mass spectrometry

This present work describes the development of a novel high throughput comparative matrix-assisted laser desorption ionization (MALDI) mass spectrometry profiling technique for endogenous compounds using a new isotope-coded label for relative quantitation of carboxylic acids. The key new aspect of this technique was a differential label, 3-hydroxymethyl-1-ethylpyrididinium iodide (HMEP), designed specifically for simultaneous quantitative MALDI analysis of two physiological states. The HMEP-d(0) and HMEP-d(5) variants of the label were applied to profiling endogenous fatty acid levels during a fish oil intervention study, using the metabolite profile of every individual person in the study as their own personal analytical reference standard. Initially, analytical figures of merit such as sensitivity, linear dynamic range, limit of quantitation, and precision were determined from the comparative quantitation experiments. Importantly, the permanently charged HMEP mass tag not only increased the ionization efficiency of the studied fatty acids but also ensured that the solution phase properties of the analytes became more similar, allowing the use of CHCA as a single MALDI matrix compound for the entire range of analytes. The label exhibited a further very unique feature; it provided complete suppression of MALDI matrix-related ions. The MALDI assay was able to generate the data much faster than conventional gas chromatography (GC) methods for fatty acids. It is shown in this study that analyzing a single sample took less than 10 s with analytical results of comparable quality to those obtained by GC.

Comprehensive analysis of the Brassica juncea root proteome in response to cadmium exposure by complementary proteomic approaches

Indian mustard (Brassica juncea L.) is known to both accumulate and tolerate high levels of heavy metals from polluted soils. To gain a comprehensive understanding of the effect of cadmium (Cd) treatment on B. juncea roots, two quantitative proteomics approaches--fluorescence two-dimensional difference gel electrophoresis (2-D DIGE) and multiplexed isobaric tagging technology (iTRAQ)--were implemented. Several proteins involved in sulfur assimilation, redox homeostasis, and xenobiotic detoxification were found to be up-regulated. Multiple proteins involved in protein synthesis and processing were down-regulated. While the two proteomics approaches identified different sets of proteins, the proteins identified in both datasets are involved in similar biological processes. We show that 2-D DIGE and iTRAQ results are complementary, that the data obtained independently using the two techniques validate one another, and that the quality of iTRAQ results depends on both the number of biological replicates and the number of sample injections. This study determined the involvement of enzymes such as peptide methionine sulfoxide reductase and 2-nitropropane dioxygenase in alternatives redox-regulation mechanisms, as well as O-acetylserine sulfhydrylase, glutathione-S-transferase and glutathione-conjugate membrane transporter, as essential players in the Cd hyperaccumation and tolerance of B. juncea.

FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides

Measurements of protein abundance and quantitative assessment of multiple post-translational modifications (PTMs) within a single protein are increasingly used to understand the control of protein activity, particularly in metazoan cells. General methods of wide applicability and precision/accuracy for quantitative estimation of protein post-translational regulation are lacking. Protein mass spectrometry has evolved from a high-throughput qualitative technique to a potentially general quantitative tool, but there are still serious limitations in dynamic range and coverage. To address some of these limitations, we introduce a novel MS-based quantitative strategy, FLEXIQuant, (Full-Length Expressed Stable Isotope-labeled Proteins for Quantification), which can track changes in relative peptide abundances as a function of PTM, and determine absolute quantity of a protein from its lysate. We examined two subunits of the anaphase-promoting complex, CDC27 and APC5, as a test of our ability to monitor quantitatively, the PTM status of several peptides over time. We find evidence of differential regulation at different sites, a phenomenon we believe will be very widespread. FLEXIQuant proved itself to be capable of serving as a general quantitative tool.

18O stable isotope labeling in MS-based proteomics

A variety of stable isotope labeling techniques have been developed and used in mass spectrometry (MS)-based proteomics, primarily for relative quantitation of changes in protein abundances between two compared samples, but also for qualitative characterization of differentially labeled proteomes. Differential (16)O/(18)O coding relies on the (18)O exchange that takes place at the C-terminal carboxyl group of proteolytic fragments, where two (16)O atoms are typically replaced by two (18)O atoms by enzyme-catalyzed oxygen-exchange in the presence of H(2)(18)O. The resulting mass shift between differentially labeled peptide ions permits identification, characterization and quantitation of proteins from which the peptides are proteolytically generated. This review focuses on the utility of (16)O/(18)O labeling within the context of mass spectrometry-based proteome research. Different strategies employing (16)O/(18)O are examined in the context of global comparative proteome profiling, targeted subcellular proteomics, analysis of post-translational modifications and biomarker discovery. Also discussed are analytical issues related to this technique, including variable (18)O exchange along with advantages and disadvantages of (16)O/(18)O labeling in comparison with other isotope-coding techniques.

De novo synthesis of trideuteromethyl esters of amino acids for use in GC-MS and GC-tandem MS exemplified for ADMA in human plasma and urine: standardization, validation, comparison and proof of evidence for their aptitude as internal standards

Asymmetric dimethylarginine (ADMA, N(G),N(G)-dimethyl-L-arginine) is an endogenous inhibitor of nitric oxide (NO) synthesis, a potential risk factor for cardiovascular diseases and a powerful biochemical parameter in clinical studies. In our previous work we have reported on a GC-tandem MS method for the accurate and precise quantification of ADMA in biological fluids using de novo synthesized [(2)H(3)]-methyl ester ADMA (d(3)Me-ADMA) as internal standard (IS). This method provides basal ADMA concentrations in biological fluids that agree with those obtained by other groups using other validated methods for ADMA. Unanimously, de novo synthesized stable-isotope labeled analogues are considered not ideal IS, because they must be prepared in a matrix different from the biological sample. Recently, [2,3,3,4,4,5,5-(2)H(7)]-ADMA (d(7)-ADMA) has become commercially available and we took this opportunity to test the reliability of the de novo synthesized d(3)Me-ADMA as an IS for ADMA in GC-tandem MS. In this article, we report on the re-validation of the previously reported GC-tandem MS method for ADMA in human plasma and urine using d(7)-ADMA as IS, and on comparative quantitative analyses of ADMA by GC-tandem MS using d(7)-ADMA and d(3)Me-ADMA. After thorough standardization of d(7)-ADMA and methods validation, we obtained by GC-tandem MS very similar ADMA concentrations in plasma and urine using d(7)-ADMA and d(3)Me-ADMA. The present study gives a proof of evidence for the aptitude of (2)H(3)-ADMA as IS in GC-tandem MS and suggests that de novo synthesis of stable-isotope labeled alkyl esters of amino acids and amino acid derivates may be a generally applicable method in mass spectrometry-based methods for amino acids. This approach is especially useful for amino acids for which no stable-isotope labeled analogues are commercially available.

The cancer secretome: a reservoir of biomarkers

Biomarkers are pivotal for cancer detection, diagnosis, prognosis and therapeutic monitoring. However, currently available cancer biomarkers have the disadvantage of lacking specificity and/or sensitivity. Developing effective cancer biomarkers becomes a pressing and permanent need. The cancer secretome, the totality of proteins released by cancer cells or tissues, provides useful tools for the discovery of novel biomarkers. The focus of this article is to review the recent advances in cancer secretome analysis. We aim to elaborate the approaches currently employed for cancer secretome studies, as well as its applications in the identification of biomarkers and the clarification of carcinogenesis mechanisms. Challenges encountered in this newly emerging field, including sample preparation, in vivo secretome analysis and biomarker validation, are also discussed. Further improvements on strategies and technologies will continue to drive forward cancer secretome research and enable development of a wealth of clinically valuable cancer biomarkers.