Capillary electrophoresis coupled to mass spectrometry for clinical diagnostic purposes

Rapid capture of biomolecules from blood via stimuli-responsive elastomeric particles for acoustofluidic separation

The detection of biomarkers in blood often requires extensive and time-consuming sample preparation to remove blood cells and concentrate the biomarker(s) of interest. We demonstrate proof-of-concept for a chip-based, acoustofluidic method that enables the rapid capture and isolation of a model protein biomarker (i.e., streptavidin) from blood for off-chip quantification. Our approach makes use of two key components - namely, soluble, thermally responsive polypeptides fused to ligands for the homogeneous capture of biomarkers from whole blood and silicone microparticles functionalized with similar, tethered, thermally responsive polypeptides. When the two components are mixed together and subjected to a mild thermal trigger, the thermally responsive moieties undergo a phase transition, causing the untethered (soluble) polypeptides to co-aggregate with the particle-bound polypeptides. The mixture is then diluted with warm buffer and injected into a microfluidic channel supporting a bulk acoustic standing wave. The biomarker-bearing particles migrate to the pressure antinodes, whereas blood cells migrate to the pressure node, leading to rapid separation with efficiencies exceeding 90% in a single pass. The biomarker-bearing particles can then be analyzed via flow cytometry, with a limit of detection of 0.75 nM for streptavidin spiked in blood plasma. Finally, by cooling the solution below the solubility temperature of the polypeptides, greater than 75% of the streptavidin is released from the microparticles, offering a unique approach for downstream analysis (e.g., sequencing or structural analysis). Overall, this methodology has promise for the detection, enrichment and analysis of some biomarkers from blood and other complex biological samples.

Reconsidering adsorption in hemodialysis: is it just an epiphenomenon? A narrative review

Since the first attempt at extracorporeal renal replacement therapy, renal replacement therapy has been constantly improved. In the field of hemodialysis, substantial efforts have been made to improve toxin removal and biocompatibility. The advent of hemodiafiltration (HDF) and, more recently, of mid cut-off membranes have contributed to management of patients with end-stage renal disease (ESRD). Although several uremic toxins have been discovered, we know little about the clinical impact of their clearance in hemodialysis patients. In addition, a great deal of progress has been made in the areas of filtration and diffusion, but the adsorptive properties of hemodialysis membranes remain under-studied. The mechanism of action of adsorption is based on the attraction between the polymer of the dialysis membrane and the solutes, through hydrophobic interactions, ionic or electrostatic forces, hydrogen bonds or van der Waals forces. Adsorption on the dialysis membrane depends on the membrane surface, pore size, structure and electric load. Its involvement in toxin removal and biocompatibility is significant, and is not just an epiphenomenon. Diffusive and convective properties cannot be improved indefinitely and high permeability membranes, despite their high performance in the clearance of many toxins, have several limitations for long-term use in hemodialysis. This review will discuss why adsorption should be reconsidered and better characterized to improve efficiency and adequacy of dialysis.

[Analysis of differentially expressed proteome in urine from non-small cell lung cancer patients]

背景与目的

筛查非小细胞肺癌（non-small cell lung cancer, NSCLC）患者尿液中差异表达蛋白，确定可用于NSCLC早期诊断、监测预后和治疗评估的生物标记物。

方法

分别收集40例已病理证实初诊NSCLC患者、8例肺部良性疾病患者和22例健康志愿者的尿液样本。利用0.9%一维十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（sodium dode-cyl sulfate polyacrylamide gel electrophoresis, 1D SDS-PAGE）技术和MS-Thermo-Orbitrap-Velos质谱分析仪对NSCLC组和非肿瘤组尿液中蛋白质进行分离、提取及识别，鉴定出NSCLC患者尿液中的差异表达蛋白。应用SPSS 20.0软件中受试者工作特征曲线（receiver operating characteristic curve, ROC）分别对其敏感性、特异性进行分析，并进行实验验证，从而确定出与NSCLC相关的生物标记物。

结果

NSCLC患者组和非肿瘤组尿液差异性表达蛋白质集中表现在90 kDa、60 kDa和20 kDa-30 kDa凝胶条带中。在NSCLC患者尿液蛋白分析中发现了4种与NSCLC相关的差异表达蛋白，包括上调蛋白LRG1、CA1和下调蛋白VPS4B、YWHAZ。这4种差异表达蛋白作为独立的NSCLC生物标记物其敏感性较低：LRG1蛋白敏感性83.0%（25/30）、特异性90.0%（18/20）；CA1蛋白敏感性60.0%（18/30）、特异性90.0%（18/20)；VPS4B蛋白敏感性73.3%（22/30）、特异性90.0%（18/20）；YWHAZ蛋白敏感性60.0%（18/30）、特异性95.0%（19/20）。而采用蛋白质组合模式对NSCLC进行筛查、诊断，则其敏感性和特异性分别可高达96.7%（29/30）和85%（17/20）。

结论

LRG1、CA1蛋白在NSCLC患者尿液中高表达，而VPS4B、YWHAZ蛋白呈低表达，差异表达蛋白均提示有可能成为用于NSCLC早期筛查、监测预后和治疗评估的生物标记物。LRG1、CA1、VPS4B和YWHAZ尿液蛋白作为单一生物标记物应用于NSCLC筛查和诊断的敏感性较低，而采用蛋白质组合模式明显优于独立模式对NSCLC的筛查和诊断，故蛋白质组合模式在临床诊疗中将更具有良好应用价值和前景。

Deamidation in ricin studied by capillary zone electrophoresis- and liquid chromatography-mass spectrometry

Deamidation in ricin, a toxin present in castor beans from the plant Ricinus communis, was investigated using capillary zone electrophoresis (CZE) and liquid chromatography coupled to high resolution mass spectrometry. Potential sites for deamidation, converting asparagine (Asn) into aspartic or isoaspartic acid (Asp or isoAsp), were identified in silico based on the protein sequence motifs and tertiary structure. In parallel, CZE- and LC-MS-based screening were performed on the digested toxin to detect deamidated peptides. The use of CZE-MS was critical for the separation of small native/deamidated peptide pairs. Selected peptides were subjected to a detailed analysis by tandem mass spectrometry to verify the presence of deamidation and determine its exact position. In the ricin preparation studied, deamidation was confirmed and located to three asparagine residues: Asn54 in the A-chain, and Asn42 and Asn60 in the B-chain. Possible in vitro deamidation occurring during sample preparation was monitored using a synthetic peptide with a known and rapid rate of deamidation. Finally, we showed that the isoelectric diversity previously reported in ricin is related to the level of deamidation.

Ionization techniques in capillary electrophoresis-mass spectrometry: principles, design, and application

A major step forward in the development and application of capillary electrophoresis (CE) was its coupling to ESI-MS, first reported in 1987. More than two decades later, ESI has remained the principal ionization technique in CE-MS, but a number of other ionization techniques have also been implemented. In this review the state-of-the-art in the employment of soft ionization techniques for CE-MS is presented. First the fundamentals and general challenges of hyphenating conventional CE and microchip electrophoresis with MS are outlined. After elaborating on the characteristics and role of ESI, emphasis is put on alternative ionization techniques including sonic spray ionization (SSI), thermospray ionization (TSI), atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), matrix-assisted laser desorption ionization (MALDI) and continuous-flow fast atom bombardment (CF-FAB). The principle of each ionization technique is outlined and the experimental set-ups of the CE-MS couplings are described. The strengths and limitations of each ionization technique with respect to CE-MS are discussed and the applicability of the various systems is illustrated by a number of typical examples.

Determination of carbohydrates in Folium Lysium Chinensis using capillary electrophoresis combined with far-infrared light irradiation-assisted extraction

In this work, a method based on capillary electrophoresis with amperometric detection and far-infrared-assisted extraction has been developed for the determination of mannitol, sucrose, glucose and fructose in Folium Lysium Chinensis, a commonly used traditional Chinese medicine. The water-soluble constituents in the herbal drug were extracted with double distilled water with the assistance of far-infrared radiations. The effects of detection potential, irradiation time, and the voltage applied on the infrared generator were investigated to acquire the optimum analysis conditions. The detection electrode was a 300-μm-diameter copper disk electrode at a detection potential of +0.65 V. The four carbohydrates could be well separated within 18 min in a 50-cm length fused-silica capillary at a separation voltage of 9 kV in a 50-mM NaOH aqueous solution. The relation between peak current and analyte concentration was linear over about three orders of magnitude with detection limits (S/N=3) ranging from 0.66 to 1.15 μM for all analytes. The results indicated that far infrared significantly enhanced the extraction efficiency of the carbohydrates in Folium Lysium Chinensis. The extraction time was significantly reduced to 7 min compared with several hours for conventional hot solvent extraction.

Mass spectrometry-based clinical proteomics: head-and-neck cancer biomarkers and drug-targets discovery

Mass spectrometry (MS)-based proteomics is a rapidly developing technology for both qualitative and quantitative analyses of proteins, and investigations into protein posttranslational modifications, subcellular localization, and interactions. Recent advancements in MS have made tremendous impact on the throughput and comprehensiveness of cancer proteomics, paving the way to unraveling deregulated cellular pathway networks in human malignancies. In turn, this knowledge is rapidly being translated into the discovery of novel potential cancer markers (PCMs) and targets for molecular therapeutics. Head-and-neck cancer is one of the most morbid human malignancies with an overall poor prognosis and severely compromised quality of life. Early detection and novel therapeutic strategies are urgently needed for more effective disease management. The characterizations of protein profiles of head-and-neck cancers and non-malignant tissues, with unprecedented sensitivity and precision, are providing technology platforms for identification of novel PCMs and drug targets. Importantly, low-abundance proteins are being identified and characterized, not only from the tumor tissues, but also from bodily fluids (plasma, saliva, and urine) in a high-throughput and unbiased manner. This review is a critical appraisal of recent advances in MS-based proteomic technologies and platforms for facilitating the discovery of biomarkers and novel drug targets in head-and-neck cancer. A major challenge in the discovery and verification of these cancer biomarkers is the typically limited availability of well-characterized and adequately stored clinical samples in tumor and sera banks, collected using recommended procedures, and with detailed information on clinical, pathological parameters, and follow-up. Most biomarker discovery studies use limited number of clinical samples and verification of cancer markers in large number of samples is beyond the scope of a single laboratory. The validation of these potential markers in large sample cohorts in multicentric studies is needed for their translation from the bench to the bedside.

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles

Saliva is a readily accessible and informative biofluid, making it ideal for the early detection of a wide range of diseases including cardiovascular, renal, and autoimmune diseases, viral and bacterial infections and, importantly, cancers. Saliva-based diagnostics, particularly those based on metabolomics technology, are emerging and offer a promising clinical strategy, characterizing the association between salivary analytes and a particular disease. Here, we conducted a comprehensive metabolite analysis of saliva samples obtained from 215 individuals (69 oral, 18 pancreatic and 30 breast cancer patients, 11 periodontal disease patients and 87 healthy controls) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS). We identified 57 principal metabolites that can be used to accurately predict the probability of being affected by each individual disease. Although small but significant correlations were found between the known patient characteristics and the quantified metabolites, the profiles manifested relatively higher concentrations of most of the metabolites detected in all three cancers in comparison with those in people with periodontal disease and control subjects. This suggests that cancer-specific signatures are embedded in saliva metabolites. Multiple logistic regression models yielded high area under the receiver-operating characteristic curves (AUCs) to discriminate healthy controls from each disease. The AUCs were 0.865 for oral cancer, 0.973 for breast cancer, 0.993 for pancreatic cancer, and 0.969 for periodontal diseases. The accuracy of the models was also high, with cross-validation AUCs of 0.810, 0.881, 0.994, and 0.954, respectively. Quantitative information for these 57 metabolites and their combinations enable us to predict disease susceptibility. These metabolites are promising biomarkers for medical screening. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-009-0178-y) contains supplementary material, which is available to authorized users.

A new CE-ESI-MS method for the detection of stable hemoglobin acetaldehyde adducts, potential biomarkers of alcohol abuse

A new CE-ESI-MS method was developed to provide a simple way to study changes to hemoglobin (HbA) induced by acetaldehyde (Ach) in vitro. Instrumental parameters were univariately optimized in order to maximize the sensitivity of the CE-ESI-MS method. The electrophoretic separations were carried out in poly-E323-coated capillaries using 60 mM formic acid raised to pH 3.0 with ammonia and containing 5% 2-propanol while the sheath liquid, 2-propanol/water (30:70) with 0.1% formic acid, was delivered at 1.0 microL/min through a coaxial sheath flow electrospray interface. The HbA was incubated with Ach for intervals up to 24 h at concentration varying in the window 0.2-20 mM. Four stable Ach-hemoglobin adducts in the hemoglobin tryptic digest were observed at the submillimolar Ach concentration and characterized by MS/MS experiments: although the alpha and beta N-amino terminal modifications were expected, the two internal ones arising, respectively, from the condensation of Ach molecules on the histidine residue in position 4 in alpha4 (i.e. the fourth peptide after tryptic digestion of alpha chain starting from amino terminal) and on the asparagine residue in position 2 in beta3, were identified for the first time. During the in vitro experiments higher concentrations of Ach were also used; however, it was not possible to identify any other stable modification of hemoglobin. Interestingly, those stable modifications are the only ones in vivo identified in the hemoglobin of moderate alcohol drinkers.

Identification of a unique urinary biomarker profile in patients with autosomal dominant polycystic kidney disease

To gain some insight into early disease progression in human autosomal dominant polycystic kidney disease (ADPKD), we analyzed the urine proteome of 41 young patients with ADPKD whose renal function was relatively preserved. Using capillary electrophoresis and mass spectrometry, we compared these results to those from age-matched healthy controls and patients with other renal diseases. There were 197 proteins with significantly altered urinary excretion; and 38 of them could be sequenced, most of which were collagen fragments. This suggests that there is high turnover of extracellular matrix proteins. Uromodulin peptides, previously implicated in tubular injury, were also found in the urine specimens. These marker proteins were found to distinguish patients from controls with a high degree of accuracy. The sensitivity and specificity of this marker set remained high in an independent validation cohort of 24 patients with ADPKD and 35 healthy controls, and even in comparisons of patients with a variety of other renal diseases or patients with kidney or bladder cancer. These findings present a potential hypothesis for the mechanisms of disease progression in ADPKD which will need to be confirmed by further studies.

Mass spectrometric analysis of body fluids for biomarker discovery

Hinging on the concept that extracellular proteins and polypeptides will provide information on the physiological state of specific organs, or even entire organisms, proteomic analysis of biological fluids for biomarker discovery has seen rapid expansion in recent years. Although multiple studies have had success using mass spectrometric analytical techniques for determination of proteins within a sample, inspection of naturally occurring species has been difficult, with most analyses using bottom-up methodology. We have applied a new fragmentation method, electron transfer dissociation (ETD), to this problem. We have previously illustrated the benefits to spectral quality and total identifications when using a combination of the complementary fragmentation techniques, ETD, and collision-activated dissociation, for analysis of naturally occurring proteins and polypeptides within biological fluids.

Poly(methyl methacrylate) microchip affinity capillary gel electrophoresis of aptamer-protein complexes for the analysis of thrombin in plasma

Thrombin generation in blood serves as an important marker for various hemostasis-related diseases and conditions. Analytical techniques currently utilized for determining the thrombin potential of patients rely primarily on the enzymatic activity of thrombin. Microfluidic-based ACE using fluorescently labeled aptamers as affinity probes could provide a simple and efficient technique for the real-time analysis of thrombin levels in plasma. In this study, aptamers were used for the analysis of thrombin by affinity microchip CGE. The CGE used a poly(methyl methacrylate) (PMMA) microfluidic device for the sorting of the affinity complexes with a linear polyacrylamide (LPA) serving as the sieving matrix. Due to the fact that the assay was run under nonequilibrium electrophoresis conditions, the presence of the sieving gel was found to stabilize the affinity complex, providing improved electrophoretic performance compared to free-solution electrophoresis. Two fluorescently labeled aptamer affinity probes, HD1 and HD22, which bind to exosites I and II, respectively, of thrombin were investigated. With an electric field strength of 300 V/cm, two well-resolved peaks corresponding to free aptamer and the thrombin-aptamer complex were obtained in less than 1 min of separation time with a run-to-run and chip-to-chip reproducibility (RSD) of migration times <10% using both aptamers. HD22 affinity assays of thrombin produced baseline-resolved peaks with favorable efficiency due to its higher binding affinity, whereas HD1 assays showed poorer resolution of the free aptamer and complex peaks. HD22 was used in determining the level of thrombin in human plasma. Assays were performed directly on plasma that was diluted to 10% v/v. Thrombin was successfully analyzed by microchip CGE at a concentration level of 543.5 nM for the human plasma sample.

A new strategy for faster urinary biomarkers identification by Nano-LC-MALDI-TOF/TOF mass spectrometry

BACKGROUND

LC-MALDI-TOF/TOF analysis is a potent tool in biomarkers discovery characterized by its high sensitivity and high throughput capacity. However, methods based on MALDI-TOF/TOF for biomarkers discovery still need optimization, in particular to reduce analysis time and to evaluate their reproducibility for peak intensities measurement. The aims of this methodological study were: (i) to optimize and critically evaluate each step of urine biomarker discovery method based on Nano-LC coupled off-line to MALDI-TOF/TOF, taking full advantage of the dual decoupling between Nano-LC, MS and MS/MS to reduce the overall analysis time; (ii) to evaluate the quantitative performance and reproducibility of nano-LC-MALDI analysis in biomarker discovery; and (iii) to evaluate the robustness of biomarkers selection.

RESULTS

A pool of urine sample spiked at increasing concentrations with a mixture of standard peptides was used as a specimen for biological samples with or without biomarkers. Extraction and nano-LC-MS variabilities were estimated by analyzing in triplicates and hexaplicates, respectively. The stability of chromatographic fractions immobilised with MALDI matrix on MALDI plates was evaluated by successive MS acquisitions after different storage times at different temperatures.Low coefficient of variation (CV%: 10-22%) and high correlation (R2 > 0.96) values were obtained for the quantification of the spiked peptides, allowing quantification of these peptides in the low fentomole range, correct group discrimination and selection of "specific" markers using principal component analysis. Excellent peptide integrity and stable signal intensity were found when MALDI plates were stored for periods of up to 2 months at +4 degrees C. This allowed storage of MALDI plates between LC separation and MS acquisition (first decoupling), and between MS and MSMS acquisitions while the selection of inter-group discriminative ions is done (second decoupling). Finally the recording of MSMS spectra to obtain structural information was focused only on discriminative ions in order to minimize analysis time.

CONCLUSION

Contrary to other classical approaches with direct online coupling of chromatographic separation and on the flight MS and/or MSMS data acquisition for all detected analytes, our dual decoupling strategy allowed us to focus on the most discriminative analytes, giving us more time to acquire more replicates of the same urine samples thus increasing detection sensitivity and mass precision.

Immunoaffinity capillary electrophoresis as a powerful strategy for the quantification of low-abundance biomarkers, drugs, and metabolites in biological matrices

In the last few years, there has been a greater appreciation by the scientific community of how separation science has contributed to the advancement of biomedical research. Despite past contributions in facilitating several biomedical breakthroughs, separation sciences still urgently need the development of improved methods for the separation and detection of biological and chemical substances. In particular, the challenging task of quantifying small molecules and biomolecules, found in low abundance in complex matrices (e.g., serum), is a particular area in need of new high-efficiency techniques. The tandem or on-line coupling of highly selective antibody capture agents with the high-resolving power of CE is being recognized as a powerful analytical tool for the enrichment and quantification of ultra-low abundance analytes in complex matrices. This development will have a significant impact on the identification and characterization of many putative biomarkers and on biomedical research in general. Immunoaffinity CE (IACE) technology is rapidly emerging as the most promising method for the analysis of low-abundance biomarkers; its power comes from a three-step procedure: (i) bioselective adsorption and (ii) subsequent recovery of compounds from an immobilized affinity ligand followed by (iii) separation of the enriched compounds. This technology is highly suited to automation and can be engineered to as a multiplex instrument capable of routinely performing hundreds of assays per day. Furthermore, a significant enhancement in sensitivity can be achieved for the purified and enriched affinity targeted analytes. Thus, a compound that exists in a complex biological matrix at a concentration far below its LOD is easily brought to well within its range of quantification. The present review summarizes several applications of IACE, as well as a chronological description of the improvements made in the fabrication of the analyte concentrator-microreactor device leading to the development of a multidimensional biomarker analyzer.

Urine in clinical proteomics

Urine has become one of the most attractive biofluids in clinical proteomics as it can be obtained non-invasively in large quantities and is stable compared with other biofluids. The urinary proteome has been studied by almost any proteomics technology, but mass spectrometry-based urinary protein and peptide profiling has emerged as most suitable for clinical application. After a period of descriptive urinary proteomics the field is moving out of the discovery phase into an era of validation of urinary biomarkers in larger prospective studies. Although mainly due to the site of production of urine, the majority of these studies apply to the kidney and the urinary tract, but recent data show that analysis of the urinary proteome can also be highly informative on non-urogenital diseases and used in their classification. Despite this progress in urinary biomarker discovery, the contribution of urinary proteomics to the understanding of the pathophysiology of disease upon analysis of the urinary proteome is still modest mainly because of problems associated to sequence identification of the biomarkers. Until now, research has focused on the highly abundant urinary proteins and peptides, but analysis of the less abundant and naturally existing urinary proteins and peptides still remains a challenge. In conclusion, urine has evolved as one of the most attractive body fluids in clinical proteomics with potentially a rapid application in the clinic.

CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics

Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. Capillary electrophoresis coupled to mass spectrometry (CE-MS), which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enabled the diagnosis, classification, and monitoring of a wide range of diseases. CE-MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level.

High-throughput DNA diagnostic measurements using capillary electrophoresis: p53, fragile X and telomerase

Capillary electrophoresis (CE) has become recognized as a powerful tool for the characterization of DNA. It has numerous advantages over slab-gel electrophoresis in that it is fast, highly reproducible and easy to automate. It is well known for its contribution to success in sequencing the human genome, but it is equally important in a wide range of forensic and pharmaceutical applications. Of these applications, CE plays a large and important role in mutation scanning and DNA sizing. From the author's laboratory, three previously published examples are given of clinical applications in this area that have benefited from the use of capillary electrophoresis: the detection of p53 mutations by single strand conformational polymorphism, the analysis of fragile X syndrome and the measurement of telomerase activity. There are many examples from other laboratories where CE has played an important role in this field. For acceptance by the medical community, there must be a clear demonstration that capillary electrophoresis can replace and improve previous slab-gel methods. In this regard, the examples given in this review help to demonstrate that CE can replace previous slab-gel methods and show that CE can improve a wide range of applications in the medical field.

Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples

A bottom-up proteomic approach, based on capillary electrophoresis (CE) in combination with matrix- assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-ToF/ToF MS), was used to analyze immunoaffinity depleted human cerebrospinal fluid (CSF) and compare it with a non-depleted sample. After enzymatic digestion and desalting, the tryptic peptides were separated by CE using PolyE-323 modified capillaries and fractionated off-line onto MALDI target plates for further analysis by MALDI-MS and MS/MS. The protein profile of the depleted sample was compared with non depleted CSF. Overall, 85 proteins were identified with 95% significance in both samples. The significance scores for proposed biomarkers, such as amyloid-like protein 1 precursor, could be increased up to 12 times after the depletion. Other proteins, often suggested to be related to neurodegenerative diseases, like amyloid beta A4 protein precursor, superoxide dismutase and apolipoprotein E precursor could only be found in the depleted CSF samples. The effect of a derivatization of tryptic peptides with 2- methoxy-4,5-dihydro-1H-imidazole reagent for protein identification with MS was also employed to increase the number of identified proteins and the sequence coverages. The results presented in this study illustrate the benefit of combining a sample pre-fractionation step and a label's ability to enhance the ionization efficiency with the potential of CE using PolyE-323 modified capillaries in the analysis of complex samples. The straight-forward approach that provides speed and simplicity resulting in high-resolution separations and low sample consumption represents an easily applicable separation technique that can serve as a complement to other currently existing analytical approaches needed in modern proteomic analysis of clinically relevant samples.

[Capillary electrophoresis coupled to mass spectrometry for proteome analysis. An innovative diagnostic method for prostate and bladder cancer]

We developed a proteomics-based technology for the non-invasive detection of urothelial and prostate carcinoma. Using capillary electrophoresis coupled to mass spectrometry, disease-specific changes in the urinary proteome were detected and subsequently relevant polypeptides were employed as disease-specific biomarkers. Here we report the results of various studies including approximately 1,000 patients with different diseases and healthy volunteers. The results of these studies revealed that prostate and urothelial carcinoma can be detected by using disease-specific polypeptide patterns. Preliminary results also indicate that the tumour stage of an urothelial carcinoma can be estimated by this approach. In conclusion, this new and non-invasive application might help to improve the diagnostic methods already available.

Practical Points in Urinary Proteomics

During the proteomic era, one of the most rapidly growing areas in biomedical research is biomarker discovery, particularly using proteomic technologies. Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics, as the urine is an ideal source for the discovery of noninvasive biomarkers for human diseases. However, there are several barriers to the success of the field and urinary proteome analysis is not a simple task because the urine has low protein concentration, high levels of salts or other interfering compounds, and more importantly, high degree of variations (both intra-individual and inter-individual variabilities). This article provides step-by-step practical points to perform urinary proteome analysis, covering detailed information for study design, sample collection, sample storage, sample preparation, proteomic analysis, and data interpretation. The discussion herein should stimulate further discussion and refinement to develop guidelines and standardizations for urinary proteome study.

Recent progress in urinary proteomics

Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.

High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine

All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.

Capillary electrophoresis and microchip capillary electrophoresis with electrochemical and electrochemiluminescence detection

Recent advances and key strategies in capillary electrophoresis and microchip CE with electrochemical detection (ECD) and electrochemiluminescence (ECL) detection are reviewed. This article consists of four main parts: CE-ECD; microchip CE-ECD; CE-ECL; and microchip CE-ECL. It is expected that ECD and ECL will become powerful tools for CE microchip systems and will lead to the creation of truly disposable devices. The focus is on papers published in the last two years (from 2005 to 2006).

Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry

In this article, we present an overview of the different strategies for sample preparation for identification by mass spectrometry (MS) of biomarkers from serum and/or plasma. We consider the effects of the variables involved in sample collection, handling and storage, and describe different approaches for removal of high abundance proteins and serum/plasma fractionation. We review the advantages and disadvantages of such techniques as centrifugal ultrafiltration, different formats for solid phase extraction, organic solvent extraction, gel and capillary electrophoresis, and liquid chromatography. We also discuss a variety of current proteomic methods and their main applications for biomarker-related studies.

Peptidomic analysis of rat urine using capillary electrophoresis coupled to mass spectrometry

We have established and validated a protocol for the peptidomic analysis of rat urine using CE coupled to MS (CE-MS). In the first experiments, the reproducibility of the CE-MS set-up and of the established preparation procedure were assessed. To establish a first rat urinary peptidome map, samples were also analyzed using CE-FT-ICR. The subsequent analysis of independent samples from two different strains (WISTAR and CD) indicated strain-specific differences, which were validated in a blinded assessment. MS/MS revealed the presence of specific fragments from well-known urinary rat peptides, such as collagens, alpha-1-antitrypsin, and serum albumin. The CE-MS-based peptidomics platform may provide novel insights into body fluids of animal models, such as rat or mice. Together with peptide identification, the technology appears to be an excellent, complimentary, and non-invasive tool to analyze toxicological or other (patho)physiological effects of pharmaceutical compounds in animal models.

The role of electrophoresis in disease biomarker discovery

There has been increased activity in the last few years in the search for disease markers using fractionation of complex biological fluids combined with MS. While electrophoretic and chromatographic separations have played a major role in this endeavor, this manuscript is limited to a review of electrophoretic methods that have been established for disease biomarker discovery. These methods include 2-DE, difference gel electrophoresis (DIGE), and CE. We define what constitutes a biomarker, identify the steps required for establishing a biomarker, and describe the parameters needed in the design of an ideal diagnostic test. The application, advantages, and limitations of CE, DIGE, and 2-DE in meeting the goal of discovering novel biomarkers is discussed in detail, along with a few selected examples that illustrate the search for biomarkers for cancer and neurological diseases.

Screening for biomarkers in plasma from patients with gangrenous and phlegmonous appendicitis using CE and CEC in combination with MS

Today a high degree of "false" appendicitis diagnoses are occurring. In this study, a screening experiment of biomarkers of two different kinds of appendicitis, gangrenous and phlegmonous, were conducted with CE and CEC coupled to MS. Plasma samples were obtained from patients pre- and post-surgery. A large amount of data was generated to be able to compare them, and chemometrics tools were utilized to visualize the differences. Indicative patterns were found for both pre- and post-surgery of the two types of inflammation as well as between them. The divergences were traced back to the MS peaks obtained in the CE- and CEC-MS setups as possible biomarkers for the two forms of appendicitis.

CE – a multifunctional application for clinical diagnosis

CE has been used widely as an analytical tool with high separation power taking advantage of size, charge-to-size ratio, or isoelectric point of various analytes. In combination with detection methods, such as UV absorption, electrochemical detection, fluorescence, or mass spectrometry (MS), it allows the separation and detection of inorganic and organic ions, as well as complex compounds, such as polypeptides, nucleic acids, including PCR amplicons from viruses or bacteria. Recent interest in identification of biomarkers of diseases using body fluids leads to development of CE-MS techniques. These applications allowed identification of new potential biomarkers for clinical diagnosis and monitoring of therapeutic interventions. In this report, we present a technical overview of various CE techniques and discuss their applications in clinical medicine.

Mass spectrometry-based "omics" technologies in cancer diagnostics

Many "omics" techniques have been developed for one goal: biomarker discovery and early diagnosis of human cancers. A comprehensive review of mass spectrometry-based "omics" approaches performed on various biological samples for molecular diagnosis of human cancers is presented in this article. Furthermore, the existing and potential problems/solutions (both de facto experimental and bioinformatic challenges), and future prospects have been extensively discussed. Although the use of present omic methods as diagnostic tools are still in their infant stage and consequently not ready for immediate clinical use, it can be envisaged that the "omics"-based cancer diagnostics will gradually enter into the clinic in next 10 years as an important supplement to current clinical diagnostics.