Proteomics and automation

Mass Dynamics 1.0: A Streamlined, Web-Based Environment for Analyzing, Sharing, and Integrating Label-Free Data

Label-free quantification (LFQ) of shotgun proteomics data is a popular and robust method for the characterization of relative protein abundance between samples. Many analytical pipelines exist for the automation of this analysis, and some tools exist for the subsequent representation and inspection of the results of these pipelines. Mass Dynamics 1.0 (MD 1.0) is a web-based analysis environment that can analyze and visualize LFQ data produced by software such as MaxQuant. Unlike other tools, MD 1.0 utilizes a cloud-based architecture to enable researchers to store their data, enabling researchers to not only automatically process and visualize their LFQ data but also annotate and share their findings with collaborators and, if chosen, to easily publish results to the community. With a view toward increased reproducibility and standardization in proteomics data analysis and streamlining collaboration between researchers, MD 1.0 requires minimal parameter choices and automatically generates quality control reports to verify experiment integrity. Here, we demonstrate that MD 1.0 provides reliable results for protein expression quantification, emulating Perseus on benchmark datasets over a wide dynamic range. The MD 1.0 platform is available globally via: https://app.massdynamics.com/.

Microproteomic sample preparation

Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).

Recent advances in robotic protein sample preparation for clinical analysis and other biomedical applications

Discovery of new protein biomarker candidates has become a major research goal in the areas of clinical chemistry, analytical chemistry, and biomedicine. These important species constitute the molecular target when it comes to diagnosis, prognosis, and further monitoring of disease. However, their analysis requires powerful, selective and high-throughput sample preparation and product (analyte) characterisation approaches. In general, manual sample processing is tedious, complex and time-consuming, especially when large numbers of samples have to be processed (e.g., in clinical studies). Automation via microtiter-plate platforms involving robotics has brought improvements in high-throughput performance while comparable or even better precisions and repeatability (intra-day, inter-day) were achieved. At the same time, waste production and exposure of laboratory personnel to hazards were reduced. In comprehensive protein analysis workflows (e.g., liquid chromatography-tandem mass spectrometry analysis), sample preparation is an unavoidable step. This review surveys the recent achievements in automation of bottom-up and top-down protein and/or proteomics approaches. Emphasis is put on high-end multi-well plate robotic platforms developed for clinical analysis and other biomedical applications. The literature from 2013 to date has been covered.

What did we learn from multiple omics studies in asthma?

More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.

Proteomics Analysis to Identify and Characterize the Biomarkers and Physical Activities of Non-Frail and Frail Older Adults

Globally, the proportion of older adults is increasing. Older people face chronic conditions such as sarcopenia and functional decline, which are often associated with disability and frailty. Proteomics assay of potential serum biomarkers of frailty in older adults. Older adults were divided into non-frail and frail groups (n = 6 each; 3 males in each group) in accordance with the Chinese-Canadian Study of Health and Aging Clinical Frailty Scale. Adults were measured for grip power and the 6-min walk test for physical activity, and venous blood was sampled after adults fasted for 8 h. Ultra-high-performance liquid chromatography-tandem mass spectrometry was used for proteomics assay. The groups were compared for levels of biomarkers by t test and Pearson correlation analysis. Non-frail and frail subjects had mean age 77.5±0.4 and 77.7±1.6 years, mean height 160.5±1.3 and 156.6±2.9 cm and mean weight 62.5±1.2 and 62.8±2.9 kg, respectively. Physical activity level was lower for frail than non-frail subjects (grip power: 13.8±0.4 vs 26.1±1.2 kg; 6-min walk test: 215.2±17.2 vs 438.3±17.2 m). Among 226 proteins detected, for 31, serum levels were significantly higher for frail than non-frail subjects; serum levels of Ig kappa chain V-III region WOL, COX7A2, and albumin were lower. The serum levels of ANGT, KG and AT were 2.05-, 1.76- and 2.22-fold lower (all p < 0.05; Figure 1A, 2A and 3A) for non-frail than frail subjects and were highly correlated with grip power (Figure 1B, 2B and 3B). Our study found that ANGT, KG and AT levels are known to increase with aging, so degenerated vascular function might be associated with frailty. In total, 226 proteins were revealed proteomics assay; levels of angiotensinogen (ANGT), kininogen-1 (KG) and antithrombin III (AT) were higher in frail than non-frail subjects (11.26±2.21 vs 5.09±0.74; 18.42±1.36 vs 11.64±1.36; 22.23±1.64 vs 9.52±0.95, respectively, p < 0.05). These 3 factors were highly correlated with grip power (p < 0.05), with higher correlations between grip power and serum levels of ANGT (r = -0.89), KG (r = -0.90), and AT (r = -0.84). In conclusion, this is the first study to demonstrate a serum proteomic profile characteristic of frailty in older adults. Serum ANGT, KG and AT levels could be potential biomarkers for monitoring the development and progression of frailty in older adults.

Immunoproteomic technology offers an extraordinary diagnostic approach for Toxoplasma gondii infection

Immunoproteomic technology offers an exceptional tool to fill the blanks that still exist in diagnosis of Toxoplasma gondii infection despite its annotated sequence. The pitfalls of serological assays and current immunoproteomic approaches are accentuated, and new approaches are presented to improve the signal and to eliminate the noise produced by blocking-specific background. This review also highlights examples where immunoproteomic studies have contributed to broaden our understanding of toxoplasmosis diagnosis. Further promising solutions, which immunoproteomic technology can grant for toxoplasmosis diagnosis are part of an intense discussion.

Studying macromolecular complex stoichiometries by peptide-based mass spectrometry

A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.

Label-free Quantification of Proteins Using Data-Independent Acquisition

In recent years the inherit problems of the traditional data-dependent acquisition mode in shotgun proteomics have been recognized. These include bias towards fragmentation of abundant peptides, stochastic effects and chimeric product ion spectra. One of the approaches to deal with these limitations is by a technique termed data-independent acquisition (DIA). This technique is comprised of several approaches, all of which relate to the parallel fragmentation of peptides in an unbiased manner, irrespective of their abundance. Presented here is one such approach termed MSE. This chapter discusses the performance from this unique acquisition mode for identification and quantification of proteins in complex biological samples.

Analytical strategies for the global quantification of intact proteins

The quantification of intact proteins is a relatively recent development in proteomics. In eukaryotic organisms, proteins are present as multiple isoforms as the result of variations in genetic code, alternative splicing, post-translational modification and other processing events. Understanding the identities and biological functions of these isoforms and how their concentrations vary across different states is the central goal of proteomics. To date, the bulk of proteomics research utilizes a "bottom-up" approach, digesting proteins into their more manageable constitutive peptides, but sacrificing information about the specific isoform and combinations of post-translational modifications present on the protein. Very specific strategies for protein quantification such as the enzyme-linked immunosorbent assay and Western blot are commonplace in laboratories and clinics, but impractical for the study of global biological changes. Herein, we describe strategies for the quantification of intact proteins, their distinct advantages, and challenges to their employment. Techniques contained in this review include the more traditional and widely employed methodology of differential gel electrophoresis and more recently developed mass spectrometry-based techniques including metabolic labeling, chemical labeling, and label-free methodologies.

Pathway based microarray analysis, utilising enzyme compounds and cascade events

BACKGROUND

Pathway based microarray analysis is an effort to integrate microarray and pathway data in a holistic analytical approach, looking for coordinated changes in the expression of sets of genes forming pathways. However, it has been observed that the results produced are often cryptic, with cases of closely related genes in a pathway showing quite variable, even opposing expression.

OBJECTIVES

We propose a methodology to identify the state of activation of individual pathways, based on our hypothesis that gene members of many pathways or modules exhibit differential expression that results from their contribution to any combination of all their constituent pathways. Therefore, the observed expression of such a gene does not necessarily imply the activation state of a given pathway where its product participates, but reflects the net expression resulting from its participation in all its constituent pathways.

METHODS

Firstly, in an effort to validate the hypothesis, we split the genes into two groups; single and multi-membership. We then determined and compared the proportion of differentially expressed genes in each group, for each experiment. In addition, we estimated the cumulative binomial probability of observing as many or more expressed genes in each group, in each experiment, simply by chance. Second, we propose a hill climbing methodology, aiming to maximise the agreement of gene expression per module.

RESULTS

We detected more frequent expression of multi-membership genes and significantly lower probabilities of observing such a high proportion of differentially expressed multi-membership genes, as the one present in the dataset. The algorithm was able to correctly identify the state of activation of the KEGG glycolysis and gluconeogenesis modules, using a number of Saccharomyces cerevisiae datasets. We show that the result is equivalent to the best solution found following exhaustive search.

CONCLUSIONS

The proposed method takes into account the multi-membership nature of genes and our knowledge of the competitive nature of our exemplar modules, revealing the state of activity of a pathway.

Multi-membership gene regulation in pathway based microarray analysis

Background

Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway.

Results

We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency.

Conclusions

We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.

Differential proteome analysis of Mycobacterium avium subsp. paratuberculosis grown in vitro and isolated from cases of clinical Johne's disease

Bovine Johne's disease (paratuberculosis), caused by Mycobacterium avium subspecies paratuberculosis, poses a significant economic problem to the beef and dairy industry worldwide. Despite its relevance, however, pathogenesis of Johne's disease is still only partially resolved. Since mycobacterial membrane proteins expressed during infection are likely to play an important role in pathogenesis, membrane-enriched fractions, namely mucosa-derived membranes (MDM) and culture-derived membranes (CDM), of M. avium subsp. paratuberculosis from three cows with clinical paratuberculosis were investigated. An initial analysis by 2D difference gel electrophoresis (2D DIGE) and MALDI-TOF-MS analysis revealed four differentially expressed proteins with only one predicted membrane protein. Due to this limited outcome, membrane preparations were subjected to a tube–gel trypsin digestion and investigated by using nanoflow-liquid-chromatography-coupled tandem MS. Based on this approach a total of 212 proteins were detected in MDM including 32 proteins of bovine origin; 275 proteins were detected in CDM; 59 % of MDM and CDM proteins were predicted to be membrane-associated. A total of 130 of the proteins were detected in both MDM and CDM and 48 predicted membrane proteins were detected in MDM from at least two cows. Four of these proteins were not detected in CDM, implying differential expression in the host. All membrane-associated proteins, especially the four identified as being differentially expressed, might be relevant targets for further analyses into the pathogenesis of bovine paratuberculosis.

A protein processing filter method for bacterial identification by mass spectrometry-based proteomics

A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposable filter unit placed inside a centrifuge vial for processing and digestion of bacterial proteins. Each processing stage allows filtration of excess reactants and unwanted byproduct while retaining the proteins. Upon addition of trypsin, the peptide mixture solution is passed through the filter while retaining the trypsin enzyme. The peptide mixture is then analyzed by LC-MS/MS with an in-house BACid algorithm for a comparison of the experimental unique peptides to a constructed proteome database of bacterial genus, specie, and strain entries. The concentration of bacteria was varied from 10 × 10(7) to 3.3 × 10(3) cfu/mL for analysis of the effect of concentration on the ability of the sample processing, LC-MS/MS, and data analysis methods to identify bacteria. The protein processing method and dilution procedure result in reliable identification of pure suspensions and mixtures at high and low bacterial concentrations.

Proteomic analysis of epicardial and subcutaneous adipose tissue reveals differences in proteins involved in oxidative stress

Epicardial adipose tissue (EAT) is an endocrine organ adjacent to coronary arteries and myocardium without anatomy barriers. Locally produced adipokines may reflect or affect to cardiovascular physiology and pathology. Our aim was to study the protein expression profiles of EAT and subcutaneous adipose tissue (SAT) to identify local candidate molecules characterizing EAT in patients with cardiovascular disease. EAT and SAT samples were collected from 55 patients undergoing heart surgery. Proteins from these tissues were separated by two-dimensional (2D) gel electrophoresis, and differences between them were identified by MALDI-TOF/TOF spectra. Differences in protein levels were further investigated by real-time RT-PCR and Western blots, and production of reactive oxygen species (ROS) in EAT and SAT was evaluated by nitroblue tetrazolium chloride assays. ROS production was higher in EAT than SAT. We have found mRNA differences for catalase, glutathione S-transferase P, and protein disulfide isomerase, and 2D Western blots additionally showed post-translational differences for phosphoglycerate mutase 1; all four are related to oxidative stress pathways. EAT suffers greater oxidative stress than SAT in patients with cardiovascular diseases and exhibits associated proteomic differences that suggest the possibility of its association with myocardial stress in these patients.

Evaluation of plasma carcinogenic markers in rat hepatic tumors models induced by rat hepatoma N1-S1 cells and benzo[a]pyrene

Benzo[a]pyrene (BaP) is a known carcinogen. Grilled or smoked meat is the major source of BaP intake for human beings. Previously, we established hepatic tumor animal models by injecting rat hepatoma N1-S1 cells or concomitant injection of N1-S1 cells and BaP into healthy Sprague-Dawley rats. In this study, we performed proteomic analyses of rat plasma collected from a hepatic tumor model and compared them to controls using a 3-10 pI range and large two dimensional gel electrophoreses. Proteomic analyses of rat plasma with hepatic tumors induced by the injection of N1-S1 cells resolved 1295 protein spots. Among them, 10 proteins were identified by ESI-MS-MS; four proteins were up-regulated and six proteins were down-regulated as compared to the controls. In addition, 1295 protein spots were also resolved from rats with hepatic tumors by the injection of N1-S1 cells plus BaP; five proteins were upregulated, and seven proteins were down-regulated. Of these 12 proteins, 10 proteins were identified by ESI-MS-MS. Out of 20 identified proteins, alpha-1-inhibitor 3 and zero beta-1 globin were down-regulated in both rats with hepatic tumors by N1-S1 cell-only and rats with hepatic tumors by the injection of N1-S1 cell plus BaP as compared to the controls. In addition, the identities of four proteins, including dermcidin, serum amyloid P-component (SAP), proteasome subunit alpha type-4 and glutathione peroxidase 3 (GPX-3) were confirmed by western blot analysis. Therefore, the importance of those proteins as candidate biomarkers for the development of hepatic tumors should be further elucidated.

Peptidomics: divide et impera

The term "peptidomics" can be defined as the systematic analysis of the peptide content within a cell, organelle, tissue or organism. The science of peptidomics usually refers to the studies of naturally occurring peptides. Another meaning refers to the peptidomics approach to protein analysis. An ancient Roman strategy divide et impera (divide and conquer) reflects the essence of peptidomics. Most effort in this field is spent purifying and dividing the peptidomes, which consist of tens, hundreds or sometimes thousands of functional peptides, followed by their structural and functional characterisation. This chapter introduces the concept of peptidomics, outlines the range of methodologies employed and describes key targets - the peptide groups which are often sought after in such studies.

Development of an efficient on-chip digestion system for protein analysis using MALDI-TOF MS

A solid-phase trypsin microreactor was constructed and operated with electrokinetically-driven flow for the digestion of proteins and coupled off-line with MALDI-TOF MS. The bioreactor was fabricated from poly(methyl methacrylate), PMMA, by hot embossing using a mold master prepared by micro-milling. The solid-phase bioreactor consisted of a 4 cm long, 200 microm wide, and 50 microm deep microfluidic channel that was populated with an array of 50 microm diameter micropost structures with a 50 microm inter-post spacing. The bioreactor was prepared by covalently attaching the proteolytic enzyme, trypsin, to the UV-modified surface of the PMMA microstructures using the appropriate coupling reagents. The performance of the system was evaluated using a set of proteins. The bioreactor provided efficient digestion of cytochrome c at a field strength of 375 V/cm, producing a reaction time of approximately 20 s to produce 97% sequence coverage for protein identification. Bovine serum albumin (BSA), phosphorylase b, and beta-casein were also assessed and the sequence coverages were 46, 63, and 79%, respectively, using the same reactor residence time. Furthermore, Escherichia coli was used as a model to demonstrate the feasibility of fingerprint analysis for intact cells using this solid-phase bioreactor.

Microfluidics with MALDI analysis for proteomics--a review

Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.

Microfluidic chips for mass spectrometry-based proteomics

Microfluidic devices coupled to mass spectrometers have emerged as excellent tools for solving the complex analytical challenges associated with the field of proteomics. Current proteome identification procedures are accomplished through a series of steps that require many hours of labor-intensive work. Microfluidics can play an important role in proteomic sample preparation steps prior to mass spectral identification such as sample cleanup, digestion, and separations due to its ability to handle small sample quantities with the potential for high-throughput parallel analysis. To utilize microfluidic devices for proteomic analysis, an efficient interface between the microchip and the mass spectrometer is required. This tutorial provides an overview of the technologies and applications of microfluidic chips coupled to mass spectrometry for proteome analysis. Various approaches for combining microfluidic devices with electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are summarized and applications of chip-based separations and digestion technologies to proteomic analysis are presented.

Fully automated two-dimensional electrophoresis system for high-throughput protein analysis

A fully automated two-dimensional electrophoresis (2DE) system for rapid and reproducible protein analysis is described. 2DE that is a combination of isoelectric focusing (IEF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is widely used for protein expression analysis. Here, all the operations are achieved in a shorter time and all the transferring procedures are performed automatically. The system completed the entire process within 1.5 h. A device configuration, operational procedure, and data analysis are described using this system.

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra

For automated production of tandem mass spectrometric data for proteins and peptides >3 kDa at >50 000 resolution, a dual online-offline approach is presented here that improves upon standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies. An integrated hardware and software infrastructure analyzes online LC-MS data and intelligently determines which targets to interrogate offline using a posteriori knowledge such as prior observation, identification, and degree of characterization. This platform represents a way to implement accurate mass inclusion and exclusion lists in the context of a proteome project, automating collection of high-resolution MS/MS data that cannot currently be acquired on a chromatographic time scale at equivalent spectral quality. For intact proteins from an acid extract of human nuclei fractionated by reversed-phase liquid chromatography (RPLC), the automated offline system generated 57 successful identifications of protein forms arising from 30 distinct genes, a substantial improvement over online LC-MS/MS using the same 12 T LTQ FT Ultra instrument. Analysis of human nuclei subjected to a shotgun Lys-C digest using the same RPLC/automated offline sampling identified 147 unique peptides containing 29 co- and post-translational modifications. Expectation values ranged from 10 (-5) to 10 (-99), allowing routine multiplexed identifications.

Protein profiling by microscale solution isoelectrofocusing (MicroSol-IEF)

Sample prefractionation is essential for more comprehensive coverage and reliable detection of low-abundance proteins in complex proteomes. An efficient and reproducible new method for sample prefractionation is microscale solution isoelectrofocusing (MicroSol-IEF), in which samples are separated into chambers defined by membranes of specific pH, yielding well resolved fractions on the basis of isoelectric point (pI). The output seamlessly interfaces with narrow-pH-range 2-D gels, enhancing data obtained from protein profiling studies, including quantitative proteome comparisons. This unit presents the MicroSol-IEF method using the ZOOM IEF Fractionator with either commercially available or custom-made pH partition membranes. Alternative configurations are possible for separating samples into different numbers of fractions with various pH ranges and volumes. A detailed method is provided for preparing custom pH membranes. In addition, methods are provided for evaluating the effectiveness of the prefractionation, using 1-D and 2-D gel electrophoresis. Approaches for quantitative protein profiling that incorporate MicroSol-IEF are also discussed.

Influence of gel dimensions on resolution and sample throughput on two-dimensional gels

To achieve high throughput and economical format of 2-D PAGE, comparison between gel size and resolution was conducted on human breast carcinoma cell line (MCF-7/AZ) proteins. SDS gel length showed a weaker influence of separation length on resolution in the second dimension, and there was little benefit of separation distances greater than 15 to 19 cm. IPG strip separation distances were very important with dramatic increase in resolution of longer gels compared with smaller gels, and maximal resolution was obtained using 18- and 24-cm IPG strips. Loading optimal amount of proteins on 2-D gels can also increase the number of detected spots. Therefore, taken together, compromise 2-D gels are crucial for higher capacity and higher throughput.

Trypsin immobilization on three monolithic disks for on-line protein digestion

The preparation and characterization of three trypsin-based monolithic immobilized enzyme reactors (IMERs) developed to perform rapid on-line protein digestion and peptide mass fingerprinting (PMF) are described. Trypsin (EC 3.4.21.4) was covalently immobilized on epoxy, carbonyldiimidazole (CDI) and ethylenediamine (EDA) Convective Interaction Media (CIM) monolithic disks. The amount of immobilized enzyme, determined by spectrophotometric measurements at 280nm, was comprised between 0.9 and 1.5mg per disk. Apparent kinetic parameters Km* and Vmax*, as well as apparent immobilized trypsin BAEE-units, were estimated in flow-through conditions using N-alpha-benzoyl-L-arginine ethyl ester (BAEE) as a low molecular mass substrate. The on-line digestion of five proteins (cytochrome c, myoglobin, alpha1-acid glycoprotein, ovalbumin and albumin) was evaluated by inserting the IMERs into a liquid chromatography system coupled to an electrospray ionization ion-trap mass spectrometer (LC-ESI-MS/MS) through a switching valve. Results were compared to the in-solution digestion in terms of obtained scores, number of matched queries and sequence coverages. The most efficient IMER was obtained by immobilizing trypsin on a CIM EDA disk previously derivatized with glutaraldehyde, as a spacer moiety. The proteins were recognized by the database with satisfactory sequence coverage using a digestion time of only 5min. The repeatability of the digestion (R.S.D. of 5.4% on consecutive injections of myoglobin 12microM) and the long-term stability of this IMER were satisfactory since no loss of activity was observed after 250 injections.

The measurement of serum ceruloplasmin is useful for diagnostic differentiation of immune thrombocytopenic purpura

BACKGROUND

To expand the criteria of immune thrombocytopenic purpura (ITP), which is a diagnosis of exclusion, we analyzed proteins separated by 1-dimensional gel electrophoresis of the retained fraction in a Con A-Sepharose column from ITP patients' sera.

METHODS

Serum samples were from 19 adult patients with chronic ITP, 9 patients with thrombocytopenia of decreased production, and 20 healthy controls. Samples were applied to a Con A-Sepharose column, and the retained fraction was subjected to 10% SDS-PAGE. The % area of each densitometric protein peak was compared between the two groups and proteins in each band were identified using LC-MS/MS.

RESULTS

Eleven protein bands were distinctly separated by 1-dimensional electrophoresis. The percent area of bands #2 and #3 were significantly higher in ITP patients than in controls. The percent area of band #2 (p<0.01) was significantly higher in ITP patients than in non-ITP patients. We identified alpha(2)-macroglobulin, ceruloplasmin (Cp), and C3 in band #2 and complement factor B in #3 band. Serum concentrations of alpha(2)-macroglobulin and Cp were significantly higher in ITP patients than in controls. Serum concentrations of Cp were significantly higher in ITP patients than in non-ITP patients (p=0.0005). Serum complement factor B concentrations were significantly higher in ITP patients and non-ITP patients than in controls. ROC analysis showed that the total percent area of bands #2 and #3, and Cp had higher diagnosis availability for ITP patients when compared with controls and non-ITP patients, respectively.

CONCLUSIONS

Measurement of Cp separated by the present method could be useful for the diagnosis of ITP in the presence of thrombocytopenia and a non- or low-inflammatory state.

Mass spectrometry in nutrition: understanding dietary health effects at the molecular level

In modern nutrition research, mass spectrometry has developed into a tool to assess health, sensory as well as quality and safety aspects of food. In this review, we focus on health-related benefits of food components and, accordingly, on biomarkers of exposure (bioavailability) and bioefficacy. Current nutrition research focuses on unraveling the link between dietary patterns, individual foods or food constituents and the physiological effects at cellular, tissue and whole body level after acute and chronic uptake. The bioavailability of bioactive food constituents as well as dose-effect correlations are key information to understand the impact of food on defined health outcomes. Both strongly depend on appropriate analytical tools to identify and quantify minute amounts of individual compounds in highly complex matrices--food or biological fluids--and to monitor molecular changes in the body in a highly specific and sensitive manner. Based on these requirements, mass spectrometry has become the analytical method of choice with broad applications throughout all areas of nutrition research. The current review focuses on selected areas of application: protein and peptide as well as nutrient and metabolite analysis.

The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells

Mass spectrometry (MS) coupled to affinity purification is a powerful approach for identifying protein-protein interactions and for mapping post-translational modifications. Prior to MS analysis, affinity-purified proteins are typically separated by gel electrophoresis, visualized with a protein stain, excised, and subjected to in-gel digestion. An inherent limitation of this series of steps is the loss of protein sample that occurs during gel processing. Although methods employing in-solution digestion have been reported, they generally suffer from poor reaction kinetics. In the present study, we demonstrate an application of a microfluidic processing device, termed the Proteomic Reactor, for enzymatic digestion of affinity-purified proteins for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Use of the Proteomic Reactor enabled the identification of numerous ubiquitinated proteins in a human cell line expressing reduced amounts of the ubiquitin-dependent chaperone, valosin-containing protein (VCP). The Proteomic Reactor is a novel technology that facilitates the analysis of affinity-purified proteins and has the potential to aid future biological studies.

Feasibility of two-dimensional gel electrophoresis used for proteomic analysis of human scleral fibroblasts

PURPOSE

This study used two-dimensional gel electrophoresis (2-DE) to analyze protein profiles for normal human scleral fibroblasts in order to provide a baseline for future study of proteomics of the sclera in experimental conditions. In addition, differences in the presence and amount of proteins from fibroblasts isolated from the anterior or posterior sclera were analyzed.

METHODS

The fibroblasts from anterior and posterior sclera of two healthy donors were cultured separately. Proteins were extracted from the cell lines, run on 2-DE, and stained by Commassie blue R-250. The gel images were analyzed to detect differences in expression levels (at least a fivefold difference in intensity) and location of the protein spots between the anterior and posterior sclera. These protein spots were trimmed from the gels, digested with trypsin, identified by MALDI mass spectrometry, and functionally categorized with human cDNA and protein databases from NCBI.

RESULTS

The number of spots detected was 455 and 453 protein spots from the anterior and posterior scleral fibroblasts, respectively. The patterns of gel maps were very similar between the anterior and posterior sclera in each donor and between the donors in either the anterior or posterior sclera. Nine proteins showed a stronger expression in the anterior sclera compared with the posterior sclera. These proteins together with the two proteins that appeared only in the anterior sclera were mainly associated with anabolic metabolism in cells. Eight proteins showed a stronger expression in the posterior sclera, and seven of them were mainly associated with catabolic metabolism in cells. Among all 19 protein spots identified as being differentially expressed between fibroblasts originally isolated from the anterior or posterior sclera, 14 proteins had a pI (3.86-7.95) and molecular weight (23-66 kDa) consistent with those found in human from the database of NCBI and from SwissProt Entry Name.

CONCLUSIONS

The distribution and levels of expression in proteins are very similar for both the anterior and posterior sclera in vitro, with only approximately 4% of the proteins demonstrating a differential level of expression (at least fivefold) between the two segments of the sclera.

Fully Automated Two-Dimensional Electrophoresis System for High-Throughput Protein Analysis

We developed a fully automated electrophoresis system for rapid and highly reproducible protein analysis. All the two-dimensional (2D) electrophoresis procedures including isoelectric focusing (IEF), on-part protein staining, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and in situ protein detection were automatically completed. The system comprised Peltiert devices, high-voltage generating devices, electrodes, and three disposable polymethylmethacrylate (PMMA) parts for IEF, reaction chambers, and SDS-PAGE. Because of miniaturization of the IEF part, rapid IEF was achieved in 30 min. A gel with a tapered edge gel on the SDS-PAGE part realized a connection between the parts without use of a gluing material. A biaxial conveyer was employed for the part relocation, sample introduction, and washing processes to realize a low-maintenance and cost-effective automation system. Performances of the system and a commercial minigel system were compared in terms of detected number, resolution, and reproducibility of the protein spots. The system achieved high-resolution comparable to the minigel system despite shorter focusing time and smaller part dimensions. The resulting reproducibility was better or comparable to the performance of the minigel system. Complete 2D separation was achieved within 1.5 h. The system is practical, portable, and has automation capabilities.

Trends in sample preparation for classical and second generation proteomics

Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.

Automating MALDI sample plate loading

We describe the design and implementation of a generic robotic solution to automate the loading of MALDI sample plates into a mass spectrometer. The soft- and hardware aspects are described together with the various safety issues that need to be addressed. The automation increases throughput by a factor of between 5- and 80-fold.

Assessing Detection Methods for Gel-Based Proteomic Analyses

Proteomic analyses using two-dimensional gel electrophoresis (2DE) depend heavily upon the quality of protein stains for sensitive detection. Indeed, detection rather than protein resolution is likely a current limiting factor in 2DE. The recent development of fluorescent protein stains has dramatically improved the sensitivity of in-gel protein detection and has enabled more accurate protein quantification. Here, we have evaluated the overall quality and relative cost of five commercially available fluorescent stains, Krypton, Deep Purple, Rubeo, Flamingo, and the most commonly used stain, Sypro Ruby (SR). All stains were found to be statistically comparable with regard to number of protein spots detected, but SR was superior with regard to fluorophore stability (e.g., capacity for repeated use of the stain solution). Notably, colloidal Coomassie Blue was also found to be comparable to SR when detected using an infrared fluorescence imaging system rather than standard densitometry. Thus, depending on available equipment and operating budgets, there are at least two high-sensitivity alternatives to achieve the best currently available in-gel protein detection: Sypro Ruby or Coomassie Blue.

Proteomics in nutrition research: principles, technologies and applications

The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.

Proteomics in cardiovascular surgery

Proteomics describes, analogous to the term genomics, the study of the complete set of proteins present in a cell, organ, or organism at a given time. The genome tells us what could theoretically happen, whereas the proteome tells us what does happen. Therefore, a genomic-centered view of biologic processes is incomplete and does not describe what happens at the protein level. Proteomics is a relatively new methodology and is rapidly changing because of extensive advances in the underlying techniques. The core technologies of proteomics are 2-dimensional gel electrophoresis, liquid chromatography, and mass spectrometry. Proteomic approaches might help to close the gap between traditional pathophysiologic and more recent genomic studies, assisting our basic understanding of cardiovascular disease. The application of proteomics in cardiovascular medicine holds great promise. The analysis of tissue and plasma/serum specimens has the potential to provide unique information on the patient. Proteomics might therefore influence daily clinical practice, providing tools for diagnosis, defining the disease state, assessing of individual risk profiles, examining and/or screening of healthy relatives of patients, monitoring the course of the disease, determining the outcome, and setting up individual therapeutic strategies. Currently available clinical applications of proteomics are limited and focus mainly on cardiovascular biomarkers of chronic heart failure and myocardial ischemia. Larger clinical studies are required to test whether proteomics may have promising applications for clinical medicine. Cardiovascular surgeons should be aware of this increasingly pertinent and challenging field of science.

Trypsin-Linked Copolymer MALDI Chips for Fast Protein Identification

For the first time, trypsin-linked copolymer poly(methyl methacrylate-co-2-amino-ethyl methacrylamide) MALDI-TOF 100-sample array chips for integrated proteomic sample preparation/measurements have been fabricated using a simple atmospheric molding protocol. The enzyme link on the polymeric chip surface has been created by covalently binding ethylene glycol disuccinate bis(sulfo-N-succinimidyl) ester with the amine functionalities of the chip well surface and subsequent reaction of the linker with 1.3 nmol trypsin. The superior performance of the new chips is demonstrated for the enzymatic digestion of individual proteins (500 fmol) of 5-60 kDa size. A mixture of 500 fmol cytochrome C, bovine serum albumin, human hemoglobin, and horse myoglobin was deposited in the trypsin-linked sample well, followed by 15-60 min of on-chip digestion. Subsequent peptide mass fingerprinting using protein-database-searching software identified all four proteins. The combination of hydrophobic pMALDI arrays and novel enzyme-linked chips minimizes sample-handling times and enhances the analytical information collected by offering intact protein mass measurements combined with enzymatic cleavage and the peptide mass fingerprint. Our concept can be readily extended to further high-throughput enzyme activity screening and protein processing.

How to comprehensively analyse proteins and how this influences nutritional research

Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, is a key platform within the "omic" technologies that also encompass genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). This review summarises protein pre-separation, identification, quantification and modification/interaction analysis and puts them into perspective for nutritional R and D. Mass spectrometry has progressed with regard to mass accuracy, resolution and protein identification performance. Separation, depletion and enrichment techniques can increasingly cope with complexity and dynamic range of proteomic samples. Hence, proteomic studies currently provide a broader, albeit still incomplete, coverage of a given proteome. Proteomics adapted and applied to nutrition and health should demonstrate ingredient efficacy, deliver biomarkers for health and disease disposition, help in differentiating dietary responders from non-responders, and discover bioactive food components.

Automated integration of monolith-based protein separation with on-plate digestion for mass spectrometric analysis of esophageal adenocarcinoma human epithelial samples

A unique approach of automating the integration of monolithic capillary HPLC-based protein separation and on-plate digestion for subsequent MALDI-MS analysis has been developed. All liquid-handling procedures were performed using a robotic module. This automated high-throughput method minimizes the amount of time and extensive labor required for traditional in-solution digestion followed by exhaustive sample cleanup and analysis. Also, precise positioning of the droplet from the capillary HPLC separation onto the MALDI plate allows for preconcentration effects of analytes for improved sensitivity. Proteins from primary esophageal Barrett's adenocarcinoma tissue were prefractionated by chromatofocusing and analyzed successfully by this automated configuration, obtaining rapid protein identifications through PMF and sequencing analyses with high sequence coverage. Additionally, intact protein molecular weight values were obtained as a means to further confirm protein identification and also to identify potential sequence modifications of proteins. This simple and rapid method is a highly versatile and robust approach for the analysis of complex proteomes.

Proteomic methods in nutrition

PURPOSE OF REVIEW

Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, is a key player in the family of -omic disciplines, which encompass genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). This review summarizes the state of the art of proteomics technology and puts it into perspective for food-related research. Learning from proteomic experiences in the pharmaceutical context, this article may help to translate proteomics into nutrition and health.

RECENT FINDINGS

Mass spectrometric technology has progressed enormously with regard to mass accuracy, resolution and peptide sequencing power. Likewise, upstream separation, depletion and enrichment techniques now allow us to deal with the large complexity and wide dynamic range of proteomic samples more efficiently. Consequently, proteomic studies now provide a broader, but still far from complete, coverage of a given proteome.

SUMMARY

Proteomics adapted and applied to the context of nutrition and health has the potential to deliver biomarkers for health and comfort, reveal early indicators of disease disposition, assist in differentiating dietary responders from non-responders, and, last but not least, discover bioactive, beneficial food components.