Methods for on-chip protein analysis

Combination of continuous digestion by peptidase and spectral similarity comparisons for peptide sequencing

Peptide sequencing is critical to the quality control of peptide drugs and functional studies of active peptides. A combination of peptidase digestion and mass spectrometry technology is common for peptide sequencing. However, such methods often cannot obtain the complete sequence of a peptide due to insufficient amino acid sequence information. Here, we developed a method of generating full peptide ladders and comparing their MS² spectral similarities. The peptide ladders, of which each component was different from the next component with one residue, were generated by continuous digestion by peptidase (carboxypeptidase Y and aminopeptidase). Then, based on the characteristics of peptide ladders, complete sequencing was realized by comparing MS² spectral similarity of the generated peptide ladders. The complete amino acid sequences of bivalirudin, adrenocorticotropic hormone, and oxytocin were determined with high accuracy. This approach is beneficial to the quality control of drug peptides as well as the identification of novel bioactive peptides.

Protein profiling in respiratory disease: techniques and impact

Multifactorial diseases such as respiratory disease call for a global analysis of such disorders. Recent advances in protein profiling techniques may allow for early diagnosis of respiratory disease, which is crucial for intervention and treatment. In order to reduce false-positive rates, clinical diagnosis requires a high degree of sensitivity and specificity to be an effective screening tool. Protein profiles identified by ProteinChip (Ciphergen Biosystems) technology coupled with mass spectrometry affords a global analysis of clinical samples and is beginning to reach acceptable levels of sensitivity and specificity. Combining the profile with another diagnostic tool enhances the effectiveness of protein profiles to classify disease. Although current efforts have centered on serum protein profiling, the local environment of the lung may be better reflected in proteins of bronchoalveolar lavage or sputum. Identification of biomarkers of disease by protein profiling analyses may lead to an understanding of the mechanisms of this disease and contribute to the discovery of new therapeutics for the prevention and treatment of disease. Advancing these analyses are techniques such as ProteinChip mass spectrometry, laser capture microdissection, tissue microarrays and fluorescently labeled antibody bead arrays, which enable the direct global analysis of complex mixtures. Effective high-throughput and ease of use of clinical testing will arrive with improvements in bioinformatics and decreases in instrumentation costs.

Synthesis and characterisation of PEG-peptide surfaces for proteolytic enzyme detection

Peptide surfaces were obtained by the covalent immobilisation of fluorescently labelled pentapeptides carboxyfluorescein-glycine-arginine-methionine-leucine-glycine, either directly or through a poly(ethylene glycol) (PEG) linker on modified silicon wafers. Each step during the preparation of the peptide surfaces was confirmed by several surface characterisation techniques. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy were used to determine the surface composition, the wafers philicity was measured by contact angle and atomic force microscopy was used to investigate the surface morphology. Exposure of the peptide surfaces to trypsin resulted in the release of a fluorescently labelled peptide product, which allowed the kinetics of the enzymatic reaction to be followed with the aid of fluorescence spectroscopy. The electrospray ionisation mass spectrometry analysis of the post-digestion solution confirmed that the pentapeptides attached to the solid support undergo specific trypsin hydrolysis at the C-terminus of the arginine residues. Detailed surface analyses before and after the enzyme action was performed using ToF-SIMS. Because of the limited accessibility of the short peptide directly attached to the surface, a quantitative yield of enzymatic hydrolysis was observed only in case when the peptide was bound through the PEG linker. The insertion of the PEG linker increased the number of immobilised peptides and the rate of enzymatic digestion which consequently improved the quality of the enzyme assays. The described approach may be used for different peptide sequences designed for other proteases.

MALDI-target integrated platform for affinity-captured protein digestion

To address immunocapture of proteins in large cohorts of clinical samples high throughput sample processing is required. Here a method using the proteomic sample platform, ISET (integrated selective enrichment target) that integrates highly specific immunoaffinity capture of protein biomarker, digestion and sample cleanup with a direct interface to mass spectrometry is presented. The robustness of the on-ISET protein digestion protocol was validated by MALDI MS analysis of model proteins, ranging from 40 fmol to 1 pmol per nanovial. On-ISET digestion and MALDI MS/MS analysis of immunoaffinity captured disease-associated biomarker PSA (prostate specific antigen) from human seminal plasma are presented.

Mass spectrometry of peptides and proteins from human blood

It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

Rapid characterization of protein chips using microwave-assisted protein tryptic digestion and MALDI mass spectrometry

We demonstrate that the microwave-assisted protein enzymatic digestion (MAPED) method can be successfully applied to the mass spectrometric characterization of proteins captured on the affinity surfaces of protein chips. The microwave-assisted on-chip tryptic digestion method was developed using a domestic microwave, completing the on-chip proteolysis reaction in minutes, whereas the previous on-chip digestion methods by incubation took hours of incubation time. For the model protein chips, antibody-presenting surfaces were prepared, where anti-α-tubulin1 and antibovine serum albumin (BSA) were immobilized on self-assembled monolayers. The resulting digestion efficiency, displaying sequence coverages of 30 and 14% for α-tubulin1 and BSA, respectively, was comparable to the previous time-consuming incubation studies. It allowed the characterization of immunosensed proteins by MASCOT search using peptide mass fingerprinting. In an example of this method for protein chip applications, BSA naturally involved in fetal bovine serum was unambiguously identified on a model protein chip by imaging mass spectrometry. This work shows that biomass spectrometry techniques can be implemented for surface mass spectrometry and biochip applications. Along with recent advances in imaging mass spectrometry, this technique will provide a new opportunity for high-speed, and thus high-throughput in the future, label-free mass spectrometric assays using protein arrays.

Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets

We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.

Biomarker analysis of stored blood products: emphasis on pre-analytical issues

Millions of blood products are transfused every year; many lives are thus directly concerned by transfusion. The three main labile blood products used in transfusion are erythrocyte concentrates, platelet concentrates and fresh frozen plasma. Each of these products has to be stored according to its particular components. However, during storage, modifications or degradation of those components may occur, and are known as storage lesions. Thus, biomarker discovery of in vivo blood aging as well as in vitro labile blood products storage lesions is of high interest for the transfusion medicine community. Pre-analytical issues are of major importance in analyzing the various blood products during storage conditions as well as according to various protocols that are currently used in blood banks for their preparations. This paper will review key elements that have to be taken into account in the context of proteomic-based biomarker discovery applied to blood banking.

Proteomic profiling in apolipoprotein E-deficient mice during atherosclerosis progression

Atherosclerosis and related complications are a major worldwide cause of human morbidity and mortality. It is advantageous to perform atherosclerosis studies in the apolipoprotein E-deficient (Apo E(-/-)) mouse model, which develops atherosclerosis very fast in comparison to humans. The aim of this study was to compare serum protein profiles in Apo E(-/-) mice during atherosclerosis progression with the data of control C57BL/6 mice. Serum proteomic analyses were performed using surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). The protein profiles obtained using three different chips, CM-10 (weak cation exchange), H50 (reversed-phase) and IMAC-30 (immobilized metal affinity capture) were statistically analyzed using the ProteinChip data manager 3.0 program. At 20 weeks of age, all Apo E(-/-) mice developed early atherosclerotic lesions. The peak intensities of 742 serum protein/peptide clusters were found to be different between the atherosclerotic and control mice groups, and the differences reached statistical significance for 107 serum protein/peptide clusters (p<0.05). This study contributes to understanding the changes in serum protein/peptide profiles during atherosclerosis development and may inform discovery of new protein biomarkers for early diagnosis of atherosclerosis.

The use of proteomics to identify novel therapeutic targets for the treatment of disease

The completion of the Human Genome Project has revealed a multitude of potential avenues for the identification of therapeutic targets. Extensive sequence information enables the identification of novel genes but does not facilitate a thorough understanding of how changes in gene expression control the molecular mechanisms underlying the development and regulation of a cell or the progression of disease. Proteomics encompasses the study of proteins expressed by a population of cells, and evaluates changes in protein expression, post-translational modifications, protein interactions, protein structure and splice variants, all of which are imperative for a complete understanding of protein function within the cell. From the outset, proteomics has been used to compare the protein profiles of cells in healthy and diseased states and as such can be used to identify proteins associated with disease development and progression. These candidate proteins might provide novel targets for new therapeutic agents or aid the development of assays for disease biomarkers. This review provides an overview of the current proteomic techniques available and focuses on their application in the search for novel therapeutic targets for the treatment of disease.

Using the protein chip interface with quadrupole time-of-flight mass spectrometry to directly identify peaks in SELDI profiles--initial evaluation using low molecular weight serum peaks

Mass spectrometric profiling, particularly in the form of SELDI, has been used in many studies, particularly in attempts to generate diagnostic serum profiles. Several studies have generated promising results but one of the limitations is the inability to identify easily potential discriminatory peaks. This may enable specific assays to be developed and increased biological insight. We describe the first systematic technical evaluation of the ProteinChip interface coupled to a tandem mass spectrometer which allows direct sequencing of peptides <6000 Da, and describe the direct sequence identification of 21 peaks commonly observed in serum samples. Additionally we describe for the first time the use of on-chip acetylation to assist in the validation of sequence identification.

Mass Spectrometry in Diagnostic Oncoproteomics

Diagnostic oncoproteomics is the application of proteomic techniques for the diagnosis of malignancies. A new mass spectrometric technology involves surface enhanced laser desorption ionization combined with time-of flight mass analysis (SELDI-TOF-MS), using special protein chips. After the description of the relevant principles of the technique, including approaches to proteomic pattern diagnostics, applications are reviewed for the diagnosis of ovarian, breast, prostate, bladder, pancreatic, and head and neck cancers, and also several other malignancies. Finally, problems and prospects of the approach are discussed.

Proteomic profiling during atherosclerosis progression: Effect of nebivolol treatment

There is a great need for the identification of biomarkers for the early diagnosis of atherosclerosis and the agents to prevent its progression. The aim of this study was to explore the effect of 24 week of nebivolol (a third-generation vasodilatory beta-blocker) treatment on serum protein profiles in Apo E(-/-) mice during atherosclerosis progression. Nebivolol treated and non-treated (the control group) groups consisted of 10 genetically modified homozygous Apo E(-/-) mice. Proteomic analyses were performed using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) in the serum samples from the nebivolol treated and non-treated Apo E(-/-) mice. The protein profiles obtained using three different chips, CM10 (weak cation-exchange), H50 (reverse phase), and IMAC30-Cu(2+) (immobilized metal affinity capture) were statistically analyzed using the ProteinChip data manager 3.0 program. At the end of 24 week of nebivolol-treatment period, a total of 662 protein/peptide clustering peaks were detected using 12 different conditions and reading with high and low intensity laser energy. The highest total number of protein/peptide clusters was found on H50 chip array. The peak intensities of 95 of the 662 protein/peptide clusters were significantly different in the nebivolol-treated atherosclerotic group in comparison to the non-treated control mice groups (P < 0.05). Forty-three protein/peptides were up-regulated (high signal intensity) while 52 protein/peptides had lower signal intensity (down-regulated) in the nebivolol-treated atherosclerotic group. The proteomic profiles of nebivolol-treated Apo E(-/-) mice were different than the control group indicating a potential role of nebivolol in atherosclerosis. Our study contributes to understand the efficacy of nebivolol on serum protein/peptide profiles during atherosclerosis development.

The application of SELDI-TOF mass spectrometry to mammalian cell culture

Surface Enhanced Laser Desorption/Ionisation Time-of-Fight Mass Spectrometry (SELDI-TOF MS) is a technique by which protein profiles can be rapidly produced from a wide variety of biological samples. By employing chromatographic surfaces combined with the specificity and reproducibility of mass spectrometry it has allowed for profiles from complex biological samples to be analysed. Profiling and biomarker identification have been employed widely throughout the biological sciences. To date, however, the benefits of SELDI-TOF MS have not been realised in the area of mammalian cell culture. The advantages in identifying markers for cell stresses, apoptosis and other culture parameters mean that these tools could help greatly to enhance monitoring and control of bioreaction process and improve the production of therapeutics. Better characterisation of culture systems through proteome analysis will allow for improved productivity and better yields.

Biomarkers of lupus nephritis determined by serial urine proteomics

Lupus nephritis is a frequent and serious complication of systemic lupus erythematosus (SLE), the treatment of which often requires the use of immunosuppressives that can have severe side effects. Here we determined the low-molecular weight proteome of serial lupus urine samples to uncover novel and predictive biomarkers of SLE renal flare. Urine from 25 flare cycles of 19 patients with WHO Class III, IV, and V SLE nephritis were obtained at baseline, pre-flare, flare and post-flare. Each sample was first fractionated to remove proteins larger than 30 kDa, then applied onto weak cation exchanger protein chips for analysis by SELDI-TOF mass spectrometry. We found 176 protein ions of which 27 were differentially expressed between specific flare intervals. On-chip peptide sequencing by integrated tandem mass spectrometry positively identified the 20 and 25 amino-acid isoforms of hepcidin, as well as fragments of alpha1-antitrypsin and albumin among the selected differentially expressed protein ions. Hepcidin 20 increased 4 months before renal flare and returned to baseline at renal flare, whereas hepcidin 25 decreased at renal flare and returned to baseline 4 months after the flare. These studies provide a beginning proteomic analysis aimed at predicting impending renal relapse, relapse severity, and the potential for recovery after SLE nephritis flare.

Use of SELDI-TOF mass spectrometry for identification of new biomarkers: potential and limitations

Surface-enhanced laser desorption time of flight mass spectrometry (SELDI-TOF-MS) is an important proteomic technology that is immediately available for the high throughput analysis of complex protein samples. Over the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis particularly with regard to the identification of novel biomarkers. Importantly, researchers have acquired a better understanding also of the limitations of this technology and various pitfalls in biomarker discovery. Bearing these in mind, great emphasis must be placed on the development of rigorous standards and quality control procedures for the pre-analytical as well as the analytical phase and subsequent bioinformatics applied to analysis of the data. To avoid the risk of false-significant results studies must be designed carefully and control groups accurately selected. In addition, appropriate tools, already established for analysis of highly complex microarray data, need to be applied to protein profiling data. To validate the significance of any candidate biomarker derived from pilot studies in appropriately designed prospective multi-center studies is mandatory; reproducibility of the clinical results must be shown over time and in different diagnostic settings. SELDI-TOF-MS-based studies that are in compliance with these requirements are now required; only a few have been published so far. In the meantime, further evaluation and optimization of both technique and marker validation strategies are called for before MS-based proteomic algorithms can be translated into routine laboratory testing.

Searching for potential biomarkers that can be used as biomarkers for diagnosing ankylosing spondylitis

Aim: Ankylosing spondylitis (AS) is a chronic systemic inflammatory rheumatic disorder that primarily affects the axial skeleton. To date there is no satisfactory biomarker for diagnosis or prognosis of AS. This study is focused on detection of potential biomarkers for the diagnosis of AS using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) with the ultimate goal of developing a progression biomarker for AS. Materials & methods: Protein profiles of sera of 38 AS patients and 38 healthy controls were obtained using ProteinChip arrays. Different arrays and conditions were compared with find out which condition resulted in the optimal discrimination of both groups. Results: Optimal discrimination was reached using weak cation exchange (CM10) and immobilized metal affinity capture coupled with copper (IMAC-Cu2+) arrays. Using a multimarker approach on protein profiles obtained with CM10 arrays resulted in a sensitivity of 66% and a specificity of 74%. Using a multimarker approach on protein profiles obtained with IMAC-Cu2+ arrays resulted in a sensitivity and specificity of 70%. Conclusions: This is the first study that shows that protein profiling in serum using SELDI-TOF-MS can be used as a diagnostic tool for AS. The biomarkers will be validated to confirm if they can be used as progression biomarkers.

Recent Advances in Real-time Mass Spectrometry Detection of Bacteria

The analysis of bio-aerosols poses a technology challenge, particularly when sampling and analysis are done in situ. Mass spectrometry laboratory technology has been modified to achieve quick bacteria typing of aerosols in the field. Initially, aerosol material was collected and subjected off-line to minimum sample treatment and mass spectrometry analysis. More recently, sampling and analysis were combined in a single process for the real-time analysis of bio-aerosols in the field. This chapter discusses the development of technology for the mass spectrometry of bio-aerosols, with a focus on bacteria aerosols. Merits and drawbacks of the various technologies and their typing signatures are discussed. The chapter concludes with a brief view of future developments in bio-aerosol mass spectrometry.

Detection of serum proteomic changes and discovery of serum biomarkers for Kashin-Beck disease using surface-enhanced laser desorption ionization mass spectrometry (SELDI-TOF MS)

The purpose of the current study was to investigate the changes of serum proteome and discover potential biomarkers for Kashin-Beck disease (KBD) using surface-enhanced laser desorption ionization mass spectrometry (SELDI-TOF MS). The serum protein profiles from 102 cases (36 KBD patients, 16 controls in KBD areas, 33 controls in non-KBD areas, and 17 osteoarthritis controls) were detected by SELDI-TOF MS and weak cation-exchange protein chip. Differently expressed peaks in KBD were identified by comparing the data among the four groups using the nonparametric Mann-Whitney test with Bonferroni correction at a significance level of 0.05. Then, those 102 cases were used to generate a classification tree as the training set, and an additional 34 cases were collected as the test set. A classification tree was generated by Biomarker Patterns Software (Ciphergen). Multiple protein changes were detected in the KBD group, including three potential biomarkers (15 886, 5336, 6113 m/z). A classification tree with three distinct proteins was generated. The classification tree was able to distinguish the KBD patients from the controls with 88.89% specificity and 86.36% sensitivity. The study demonstrates that marked serum proteomic changes exist in KBD. The proteins represented by the differently expressed peaks are candidate biomarkers for KBD.

Proteomics and heart disease: identifying biomarkers of clinical utility

Cardiovascular disease is the leading cause of mortality and morbidity in the industrialized world. Total worldwide deaths due to this disease are currently estimated at 17 million per year, and this number is expected to increase over the next several decades. To address this epidemic, a major effort has begun to develop new cardiovascular disease markers through the use of proteomic analysis, the global study of proteins. This review discusses strategies, recent technological advances and other issues in plasma/serum biomarker discovery for cardiovascular diseases. Emphasis lies on the needs for standardizing specimen collection, methods for reducing plasma proteome complexity to subproteomes, selection of appropriate technology platforms and strategies to evaluate candidates by multiplexed immune assays. The overall goal of this effort is to identify serum biomarkers for diagnosis, therapeutic monitoring and risk stratification of cardiovascular diseases.

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

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

Complete chemical and enzymatic treatment of phosphorylated and glycosylated proteins on ProteinChip arrays

A simple and quick protocol for chemical treatment, enzymatic digestion, and subsequent identification of proteins on ProteinChip arrays is presented. Chicken ovalbumin, bovine fetuin and a heavily posttranslationally modified protein, human epidermal growth factor receptor extracellular domain, were employed as model proteins to evaluate the novel protocol. The chemical treatment includes denaturation, reduction, and alkylation, while enzymatic digestion encompasses deglycosylation, dephosphorylation, and digestion by various proteases. All reactions were carried out on-chip in a sequential fashion. Peptide mass fingerprinting identified several peptides derived from the three proteins. This protocol was also applied to the analysis of urinary proteins from a male rat with puromycin-induced proteinuria. alpha-2u-Globulin, the major urinary protein in the normal male rat and albumin, the most abundant in the treated animal, were readily identified. This procedure demonstrates that complete on-chip treatment can be used for rapid protein identification and structural characterization.

A proteomic primer for the clinician

Proteomics is a rapidly developing field and it opens new horizons in many research areas of life sciences. In the field of medicine, proteomics promises to accelerate the discovery of new drug targets and protein disease markers useful for in vitro diagnosis. In this article, we review the current proteomics technologies for biomarker discovery and validation, which include two-dimensional gel electrophoresis, one- and two-dimensional liquid chromatography, and proteomic microarrays. We will also review proteomic strategies for protein-protein interactions and identification of post-translational modifications. Selection of the more effective technology or combination of technologies is required to maximize the interpretation and utility of the data.

In situ AP/MALDI-MS characterization of anchored matrix metalloproteinases

Several different procedures are available for the immobilization of proteins on solid supports, as many advantages derive from this approach, such as the possibility to develop new protein solid-state assays. Enzymes that are anchored on gold surfaces can interact with several different molecules in a tag-free environment, opening the way to surface plasmon resonance (SPR) investigations. Nevertheless, it is often important to know the identity of the affinity-retained analyte, and mass spectrometric analysis, via its unique molecular mass identification, represents a very valuable complementary method. There are many pieces of evidence to suggest that matrix metalloproteinases (MMPs) are involved in normal and pathological processes, including embryogenesis, wound healing, inflammation, arthritis and cancer, but presumably also exhibiting other functions. The search for new inhibitors of MMPs has prompted research towards the development of new solid-state assays for the rapid evaluation of MMP activity. We have already reported the possibility of measuring the activity of MMP-1 anchored on solid support by coupling SPR with ESI-MS analysis. In this work, we show the in situ atmospheric pressure (AP) MALDI-MS characterization of MMPs anchored on a gold chip with known surface coverage. The study extends the MS analysis to different proteins, and sequence coverage is reported for different digestion and MS procedures.

Peptide and protein profiles in serum and follicular fluid of women undergoing IVF

BACKGROUND

Proteins and peptides in human follicular fluid originate from plasma or are produced by follicular structures. Compositional changes reflect oocyte maturation and can be used as diagnostic markers. The aim of the study was to determine protein and peptide profiles in paired serum and follicular fluid samples from women undergoing IVF.

METHODS

Surface-enhanced laser desorption and ionization-time of flight-mass spectrometry (SELDI-TOF-MS) was used to obtain characteristic protein pattern.

RESULTS

One hundred and eighty-six individual MS signals were obtained from a combination of enrichment on strong anion exchanger (110), weak cation exchanger (52) and normal phase surfaces (24). On the basis of molecular masses, isoelectric points and immunoreactivety, four signals were identified as haptoglobin (alpha(1)- and alpha(2)-chain), haptoglobin 1 and transthyretin (TTR). Immunological and MS characteristics of the TTR : retinol-binding protein (RBP) transport complex revealed no microheterogeneity differences between serum and follicular fluid. Discriminatory patterns arising from decision-tree-based classification and regression analysis distinguished between serum and follicular fluid with a sensitivity and specificity of 100%.

CONCLUSIONS

Quantitative and qualitative differences indicate selective transport processes rather than mere filtration across the blood-follicle barrier. Identified proteins as well as characteristic peptide and/or protein signatures might emerge as potential candidates for diagnostic markers of follicle and/or oocyte maturation and thus oocyte quality.

A method for C-terminal sequence analysis in the proteomic era (proteins cleaved with cyanogen bromide)

There is growing interest in the overall study of post-translational modifications (PTMs) of proteins. Beside phosphorylation and glycosylation, truncations of the nascent polypeptide chain at the N or C termini are by far the most common types of PTMs found in proteins. However, little attention has been paid to the development of approaches that allow a systematic analysis of these proteolytic processing events. Here we present a protocol that allows the identification of the C-terminal sequences of proteins. A peptide mixture is generated by cleavage of the protein with cyanogen bromide and is incubated with carboxypeptidase Y. The enzyme is only able to act on the C-terminal fragment, because this is the only peptide without a homoserine lactone residue at its C terminus. The resulting fragments, forming a peptide ladder, are analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The entire protocol, including the CNBr cleavage, takes 21 h and can be applied to proteins purified either by SDS-PAGE or by 2D PAGE or in solution.

Proteomic study of plasma proteins in pregnant women with asthma

OBJECTIVE AND BACKGROUND

The course of asthma may be altered during pregnancy with at least one-third of women experiencing a worsening of asthma and 20% having an exacerbation during pregnancy. This study used the novel proteomic technique, surface-enhanced laser desorption ionization-time of flight mass spectrometry to determine if the presence of asthma during pregnancy was associated with alterations in plasma proteins.

METHODS

Plasma collected from healthy (n = 23) and asthmatic (n = 27) pregnant women at 18 and 30 weeks gestation was applied to strong anion exchange (SAX2), weak cation exchange (WCX2) and immobilized metal affinity capture (IMAC-Cu(2+)) chips. Mass analysis was conducted using Ciphergen Protein Biology System IIc and significant differences in individual peak intensities between groups determined.

RESULTS

At 18 weeks gestation, 91 peaks were significantly different between pregnant women with and without asthma, representing 28% of the total peaks identified. At 30 weeks gestation, 51 peaks were significantly different. There were two peaks that were significantly different between groups at both 18 and 30 weeks gestation and expressed at a similar level at both time points. One was increased in asthmatics (MW = 6444 Da) whereas the other decreased in asthmatics compared with non-asthmatic women (MW = 1846 Da).

CONCLUSIONS

This study demonstrated that there are differences in protein patterns between pregnant women with and without asthma. Other techniques are needed to define the molecular species and classify pathophysiological significance. Surface-enhanced laser desorption ionization-time of flight mass spectrometry has potential as a tool to monitor disease progression in situations such as pregnancy.

An ecotoxicoproteomic approach (SELDI-TOF mass spectrometry) to biomarker discovery in crab exposed to pollutants under laboratory conditions

Ciphergen ProteinChip Technology is a proteomic tool, used for the discovery of new and sensitive biomarkers. This approach was used to evaluate the protein profile of crabs exposed to various pollutants. Two different exposure experiments were performed: spider crabs (Hyas araneus) were exposed for 3 weeks to diallyl phatalate (DAP), bisphenol A (BisA) and polybrominated diphenyl ether (PBDE-47), while shore crabs (Carcinus maeanas) were exposed to crude oil, crude oil spiked with alkylphenols (APs) and 4-nonylphenol (NP). Gender and species-related protein pattern alterations were observed and compared to controls. Results showed different responses to pollutants by the two species. Major disruption in protein peak expression was observed in samples exposed to mixtures of pollutants, i.e. oil spiked with APs. Compared to shore crab, spider crab species showed a lower degree of response in terms of number of altered protein peaks following exposure. In general, female individuals of both species showed a larger number of significantly altered proteins compared to males. Data analysis by non-metric multi-dimensional scaling (MDS) was performed. Bi-dimesional-MDS plots revealed a good separation of groups for both spider and shore crabs. In some cases, a good discrimination can also be observed between the two genders within each treatment. Results highlight the potential of crabs as sentinel organisms for the aquatic environment. The results indicate that SELDI-ToF technology is a powerful tool to discover protein expression signatures for different pollutants and sex dependent responses.

Teaching molecular genetics: Chapter 3--Proteomics in nephrology

The novel discipline of proteomics has experienced a rapid growth in the recent past and has great potentials for the future. The study of proteins on a genomic scale enables a large number of proteins to be analysed simultaneously. Moreover, proteomic analysis reveals the presence of protein isoforms and post-translational modifications, both of which have the potential to regulate protein complex formation, activity and function. As such, the assessment of the proteome, unlike genomic analysis, provides a view of biological processes at their level of occurrence. The knowledge thus gained is important not only for a better understanding of renal physiology and pathophysiology, but also for the identification of disease markers and the development of new therapies. This review applies the science of proteomics to nephrology: our aim is to give an overview of the discipline, providing background information and outlining the scope, advantages and limitations of proteomics.

Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry

Recently, the focus of cancer research has expanded from genetic information in the human genome to protein expression analyses. Because this 'proteome' reflects the state of a cell, tissue or organism more accurately, much is expected from proteomics to yield better tumour markers for disease diagnosis and therapy monitoring. Some current proteomic technologies are particularly suitable for protein profiling in the search for new biomarkers. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry has been used frequently, highlighting many new proteins as biomarkers (e.g. for ovarian, breast, prostate and colorectal cancer). However, it is becoming increasingly recognized that reproducibility and validation of these biomarkers should be addressed carefully, as should their origin and identity. If these efforts are made, protein profiling can contribute to the better diagnosis of patients and the optimization of their treatment.

New mass spectrometric assay for angiotensin-converting enzyme 2 activity

A novel assay was developed for evaluation of mouse angiotensin-converting enzyme (ACE) 2 and recombinant human ACE2 (rACE2) activity. Using surface-enhanced laser desorption/ionization time of flight mass spectrometry (MS) with ProteinChip Array technology, ACE1 and ACE2 activity could be measured using natural peptide substrates. Plasma from C57BL/6 mice, kidney from wild-type and ACE2 knockout mice, and rACE2 were used for assay validation. Plasma or tissue extracts were incubated with angiotensin I (Ang I; 1296 m/z) or angiotensin II (Ang II; 1045 m/z). Reaction mixtures were spotted onto the ProteinChips WCX2 and peptides detected using surface-enhanced laser desorption/ionization time of flight MS. MS peaks for the substrates, Ang I and Ang II, and the generated peptides, Ang (1-7) and Ang (1-9), were monitored. The ACE2 inhibitor MLN 4760 (0.01 to 100 micromol/L) significantly inhibited rACE2 activity (IC50=3 nmol/L). Ang II was preferably cleaved by rACE2 (km=5 mumol/L), whereas Ang I was not a good substrate for rACE2. There was no detectable ACE2 activity in plasma. Assay specificity was validated in a model of ACE2 gene deletion. In kidney extract from ACE2-deficient mice, there was no generation of Ang (1-7) from Ang II. However, Ang (1-7) was produced when Ang I was used as a substrate. In conclusion, we developed a specific and sensitive assay for ACE2 activity, which used the natural endogenous peptide substrate Ang II. This approach allows for the rapid screening for ACE2, which has applications in drug testing, high-throughput enzymatic assays, and identification of novel substrates/inhibitors of the renin-angiotensin system.

Recent developments in capillary electrophoresis and capillary electrochromatography of peptides

The article gives a comprehensive review on the recent developments in the applications of high-performance capillary electromigration methods, zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography, to analysis, preparation, and physicochemical characterization of peptides. The article presents new approaches to the theoretical description and experimental verification of electromigration behavior of peptides, covers the methodological aspects of capillary electroseparations of peptides, such as rational selection of separation conditions, sample preparation, suppression of peptide adsorption, new developments in individual separation modes, and new designs of detection systems. Several types of applications of capillary electromigration methods to peptide analysis are presented: conventional qualitative and quantitative analysis, purity control, determination in biomatrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid and sequence analysis, and peptide mapping of proteins. Some examples of micropreparative peptide separations are given and capabilities of capillary electromigration techniques to provide important physicochemical characteristics of peptides are demonstrated.

The effect of maternal asthma on placental and cord blood protein profiles

OBJECTIVE

We conducted a comparative proteomic analysis of placental and umbilical cord blood proteins using surface-enhanced laser desorption ionization-time of flight mass spectrometry (SELDI-TOF MS) to examine the associations among asthma, fetal gender, and protein profiles.

METHODS

Placental tissue and umbilical vein plasma were collected from 10 healthy and 20 asthmatic women. Placental proteins were extracted using phosphate-buffered saline containing protease inhibitors. Samples were applied to the surfaces of strong anion exchange (SAX2), weak cation exchange (WCX2) and immobilized metal affinity capture (IMAC-Cu(2+)) chips. Mass analysis was conducted using a Ciphergen Protein Biology System IIc (Freemont, CA), and differences in individual peak intensities between groups were determined.

RESULTS

Fourteen placental peaks were significantly different between asthmatic and non-asthmatic women (seven more highly expressed and seven less highly expressed). Ten umbilical cord blood peak differences were identified, with four peaks more highly expressed and six peaks less highly expressed in asthmatics. Four placental and three umbilical cord blood proteins differed significantly between male and female fetuses. Two placental and five umbilical cord blood peaks were specifically increased in a subgroup of samples collected from asthmatic women who did not use inhaled glucocorticoids and were pregnant with a female fetus, a group previously found to have altered placental function.

CONCLUSIONS

This study demonstrates the abilities of the SELDI technique as a tool for protein profiling in tissue or plasma. Further work to positively identify the candidate peptides found in this study may provide a greater understanding of the placental mechanisms leading to alterations in fetal growth in patients with bronchial asthma.

The potential of ecotoxicoproteomics in environmental monitoring: biomarker profiling in mussel plasma using ProteinChip array technology

New global technologies, allowing simultaneous analysis of thousands of genes, proteins, and metabolites (so-called "omics" technologies), are being adopted rapidly by industry, academia, and regulatory agencies. This study evaluated the potential of proteomics in ecotoxicological research (i.e., ecotoxicoproteomics). Filter-feeding mussels (Mytilus edulis) were exposed continuously for 3 wk to oil, or oil spiked with alkylphenols and extra polycyclic aromatic hydrocarbons. The influence of chronic exposure on mussel plasma protein expression was investigated utilizing ProteinChip array technology in combination with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF MS). Results indicated that exposure to spiked oil had a more significant effect on protein expression in mussels than oil alone. In total, 83 mass peaks (intact or modified proteins/peptides) were significantly altered by spiked oil, while 49 were altered by oil. In exposed organisms, the majority of peaks were upregulated compared to controls (i.e., 69% in oil and 71% in spiked oil). Some peaks (32 in total) were affected by both treatments; however, the degree of response was higher in the spiked oil group for 25 of the 32 commonly affected features. Additionally, certain peaks revealed exposure- or gender-specific responses. Multivariate analysis with regression tree-based methods detected protein patterns associated with exposure that correctly classified masked samples with 90-95% accuracy. Similarly, 92% of females and 85% of males were correctly classified (independent of exposure). Results indicate that proteomics have the potential to make a valuable contribution to environmental monitoring and risk assessment.

Preliminary study on proteomics of gastric carcinoma and its clinical significance

AIM: To explore the preliminary identification of serum protein pattern models that may be novel potential biomarkers in the detection of gastric cancer.

METHODS: A total of 130 serum samples, including 70 from patients with gastric cancer and 60 from healthy adults, were detected by surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF-MS). The data of spectra were analyzed by Biomarker Patterns Software (BPS). Thirty serum samples of gastric cancer patients and 30 serum samples of healthy adults were grouped into the training group to build models, and the other 70 samples were used to test and evaluate the models. The samples of the test group were judged only with their peaks’ height and were separated into cancer group or healthy control group by BPS automatically and the judgments were checked with the histopathologic diagnosis of the samples.

RESULTS: Sixteen mass peaks were found to be potential biomarkers with a significant level of P<0.01. Among them, nine mass peaks showed increased expression in patients with gastric cancer. Analyzed by BPS, two peaks were chosen to build the model for gastric cancer detection. The sensitivity, specificity, and accuracy of the model were 90%, 36/40, 86.7%, 26/30, and 88.6%, 62/70, respectively, which were greatly higher than those of clinically used serum biomarkers CEA (carcinoembryonic antigen), CA19-9 and CA72-4. Stage I/II gastric cancer samples of the test group were all judged correctly.

CONCLUSION: The novel biomarkers in serum and the established model could be potentially used in the detection of gastric cancer. However, large-scale studies should be carried on to further explore the clinical impact on the model.

Effects of multipurpose contact lens solutions on the protein composition of the tear film

OBJECTIVES

To analyze the influence of multipurpose contact lens cleaning solutions on tear proteins. Changes in tear film protein profiles of contact lens wearers who used several marketed brands of multipurpose contact lens care solutions, were assessed by ProteinChip analysis.

METHODS

Three studies were conducted. Study I was a comparison of Complete and OptiFree multipurpose solutions. Study II was a study with Complete Moisture Plus solution, Study II was a comparison of Renu and Solocare contact lens solutions. Wearers of soft contact lenses were assigned to use the contact lens care solutions for 4 weeks. Non-contact lens wearing patients were used as controls. Tear samples of each participant were analyzed with the ProteinChip (SELDI-TOF) system. Multivariate statistical analysis and artificial neural networks were used to determine the tear protein profiles of each study group.

RESULTS

Before starting the use of the solutions, the tear protein composition in all contact lens wearers deviated from the tear composition of the non-contact lens wearing controls. After 4 weeks of using the different care regimens, the tear protein composition of the patients using Complete or Complete Moisture Plus solutions tended to move toward that of the non-contact lens wearing controls. The tear protein composition of patients using the OptiFree, Renu or Solocare solutions did not undergo a measureable change in the protein level.

CONCLUSIONS

The ProteinChip system can analyze protein profiles for large-scale applications as in clinical studies. Two multipurpose solutions, Complete and Complete Moisture Plus, demonstrated a beneficial effect on the tear proteins in contact lens wearers.

Analysis of human blood serum using the off-line coupling of capillary isoelectric focusing to matrix-assisted laser desorption/ionization time of flight mass spectrometry

Off-line coupling of capillary IEF (CIEF) with matrix-assisted laser desorption/ionization mass spectrometry was utilized for the analysis of human blood serum. Serum proteins were initially separated by CIEF, and fractions of the isoelectric separation were eluted sequentially to a MALDI-TOF MS sample target. During pressure elution of the CIEF sample, voltage was maintained across the capillary system utilizing a sheath flow arrangement to minimize band broadening induced by the laminar flow field. Both pI and mass information were obtained from the complex biological sample, similar to traditional 2-DE techniques, and the platform was faster (hours versus days), more automatable, and simpler than 2-DE. The volume of raw sample present in the actual analysis was approximately 100 nL, making this technique well suited for very rare specimens. Additionally, the speed and simplicity of the technology make it an attractive technique for performing initial comparative analyses of complex samples.

Novel mass spectrometric methods for evaluation of plasma angiotensin converting enzyme 1 and renin activity

This article demonstrates the applicability of quantitative proteomics to assays of proteolytic enzyme activity. A novel assay was developed for measurement of renin and angiotensin-converting enzyme (ACE) activity in plasma. The method was validated in animal models associated with alterations of the renin angiotensin system (RAS). Using surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS) with a ProteinChip Array technology, plasma renin and ACE1 could be measured in <0.5 microL of plasma. Plasma is incubated with peptide substrates for renin and ACE, tetradecapeptide (TDP), and angiotensin I (Ang I), respectively. The reactions mixtures are spotted onto the ProteinChip WCX2 and detected using SELDI-TOF-MS. Peak height or area under curve for TDP, Ang I, and angiotensin II (Ang II) peaks are measured. There was a linear relationship between disappearance of substrate and appearance of products for both renin and ACE (R2=0.95 to 0.98). ACE1 activity was blocked with chelating agents (EDTA and 1,10 phenanthrolene), indicating action of a metalloprotease. The ACE1 inhibitor, captopril, selectively blocked ACE1. Renin activity was specifically blocked with renin inhibitor and was not affected by phenanthrolene or captopril. Animal models tested were Ang AT1a receptor-deficient and streptozotocin (STZ) diabetic mice. Plasma renin activity was increased >2-fold in AT1a(-/-) as compared with AT1a(+/+). In STZ diabetic mice, ACE1 was increased 2-fold as compared with controls. The advantage of the method is that it is tagless, does not require additional purification steps, and is extremely sensitive. The approach can be multiplexed and used for identification of novel substrates/inhibitors of the RAS.

Protéomique et auto-anticorps

Autoimmune response is diverse. This diversity is thought not to take place at the beginning of the autoimmune process but to occur as the disease evolves. It is mainly the consequence of the so-called epitope-spreading phenomenon and of the cross-reactivity of antibodies. Analysing autoantibody repertoire constitutes a powerful means to understand physiopathological processes at work in various diseases, mainly autoimmune diseases. In particular this analysis opens the way to precisely identify autoantigens and their changes in various pathological situations, and allows providing new biological markers in chronic inflammatory diseases. New methodologies have recently emerged for the analysis of the autoantibody repertoire in a given individual. They propose diagnostic approaches no more related upon few markers but founded upon analysis of global changes of the antibody repertoire. They belong to methodologies called target-oriented proteomics. Their common feature is to isolate autoantigens by means of affinity chromatography based upon antibody/antigen reactions. Autoantibodies to be studied interact with a protein substratum susceptible to include autoantibody targets. These interactions take place on solid macro- or microsurfaces, i.e. membrane filters or chips. Several strategies can be used for locating the specific autoantibody/autoantigen complexes and for identifying behind autoantigens. In this paper three approaches, namely, the recombinant protein chips, the SELDI techniques and the 2-D gel electrophoresis linked to mass spectrometry are described and compared.