Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins

A novel microscale preparative gel electrophoresis system

A novel microscale preparative gel electrophoresis system is designed and manufactured for protein separation and preparation.

Free-flow electrophoresis in proteome sample preparation

An aim of proteome research is to identify the entire complement of proteins expressed in defined cell types of humans, animals, plants, and microorganisms. The approach requires searching for low abundant or even rarely expressed proteins in many cell types, as well as the determination of the protein expression levels in subcellular compartments and organelles. In recent years, rather powerful MS technologies have been developed. At this stage of MS device development, it is of highest interest to purify intact cell types or isolate subcellular compartments, where the proteins of interest are originating from, which determine the final composition of a peptide mixture. Free-flow electrophoresis proved to be useful to prepare meaningful peptide mixtures because of its improved capabilities in particle electrophoresis and the enhanced resolution in protein separation. Sample preparation by free-flow electrophoresis mediated particle separation was preferentially performed for purification of either organelles and their subspecies or major protein complexes. Especially, the introduction of isotachophoresis and interval zone electrophoresis improved the purity of the gained analytes of interest. In addition, free-flow IEF proved to be helpful, when proteins of low solubility, obtained, e.g. from cell membranes, were investigated.

Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome

In the last decade, there has been a dramatic progress in separation techniques, mass spectrometry, and bioinformatics, and this progress has significantly improved the techniques on protein analysis. However, the analysis of low-abundance proteins is still challenging because of the limited performance in the method of choice compared to the complexity and the vast dynamic range of biological samples. Since this issue is a big obstacle in most proteomics investigations, great interest has been paid recently to various techniques, such as multi-dimensional analysis, specific peptide selection, high-abundance protein depletion, ligand library treatment, to address this challenge. Therefore, here, the author reviews recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome, mainly focusing on their methods and perspectives.

MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma

A highly-multiplexed MRM-based assay for determination of cardiovascular disease (CVD) status and disease classification has been developed for clinical research. A high-flow system using ultra-high performance LC and an Agilent 6490 triple quadrupole mass spectrometer, equipped with an ion funnel, provided ease of use and increased the robustness of the assay. The assay uses 135 stable isotope-labeled peptide standards for the quantitation of 67 putative biomarkers of CVD in tryptic digests of whole plasma in a 30-min assay. Eighty-five analyses of the same sample showed no loss of sensitivity (<20% CV for 134/135 peptides) and no loss of retention time accuracy (<0.5% CV for all peptides). The maximum linear dynamic range of the MRM assays ranged from 10(3) -10(5) for 106 of the assays. Excellent linear responses (r >0.98) were obtained for 117 of the 135 peptide targets with attomole level limits of quantitation (<20% CV and accuracy 80-120%) for 81 of the 135 peptides. The assay presented in this study is easy to use, robust, sensitive, and has high-throughput capabilities through short analysis time and complete automated sample preparation. It is therefore well suited for CVD biomarker validation and discovery in plasma.

Validation of free flow electrophoresis as a novel plasma and serum processing and fractionation method in biobanking

Free flow electrophoresis (FFE) is a fractionation method, based on isoelectric focusing (IEF). We validate the reproducibility of the method and show that it can be applied by biobanks in order to fractionate fluid biospecimens efficiently and reproducibly and to facilitate downstream proteomic applications. We also propose a simple method allowing researchers to assess the reproducibility of each FFE run.

Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: an NCI-CPTC initiative perspective

Proteomics holds great promise in personalized medicine for cancer in the post-genomic era. In the past decade, clinical proteomics has significantly evolved in terms of technology development, optimization and standardization, as well as in advanced bioinformatics data integration and analysis. Great strides have been made for characterizing a large number of proteins qualitatively and quantitatively in a proteome, including the use of sample fractionation, protein microarrays and MS. It is believed that differential proteomic analysis of high-quality clinical biospecimen (tissue and biofluids) can potentially reveal protein/peptide biomarkers responsible for cancer by means of their altered levels of expression and/or PTMs. Multiple reaction monitoring, a multiplexed platform using stable isotope dilution-MS with sensitivity and reproducibility approaching that of traditional ELISAs commonly used in the clinical setting, has emerged as a potentially promising technique for next-generation high-throughput protein biomarker measurements for diagnostics and therapeutics.

Multi-dimensional liquid chromatography in proteomics--a review

Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments.

Multicolumn separation platform for simultaneous depletion and prefractionation prior to 2-DE for facilitating in-depth serum proteomics profiling

In this report, we describe an integrated fluidic platform composed of tandem affinity columns for the depletion of high-abundance proteins from human serum and on-line fractionation/concentration of medium- and low-abundance proteins by tandem immobilized metal-ion affinity chromatography (IMAC) columns and reversed phase (RP) column for in-depth proteomics analysis. The depletion columns were based on monolithic polymethacrylate with surface immobilized protein A, protein G', and antibodies for depleting the top 8 high-abundance proteins. The IMAC fractionation/concentration columns consisted of monolithic stationary phases with surface bound iminodiacetic acid (IDA) chelated with Zn2+, Ni2+ and Cu2+, while the RP column was packed with nonpolar polymer beads. The integrated multicolumn fluidic platform was very effective in reducing simultaneously both the dynamic range differences among the protein constituents of serum and the complexity of the proteomics samples, thus, facilitating the in-depth proteomics analysis by 2-DE followed by MALDI-TOF and LC-MS/MS. In fact, the number of detected spots was approximately 1450 using SYPRO fluorescent stain from which 384 spots were subsequently detected by Coomassie Blue. Since the investigation was simply a proof of concept, 295 proteins were readily identified in some selected spots by MALDI-TOF and LC-MS/MS.

Enhancing mass spectrometry based serum profiling by a combination of free flow electrophoresis and ClinProt

Pre-fractionation of serum specimen is a precondition for a reliable and sensitive proteomic analysis, but systemic variation of various techniques impairs the pre-analytical workflow and at least assay reproducibility. In the present study we introduce and evaluate a two-dimensional fractionation approach combining liquid-based isoelectric focusing (IEF) and affinity chromatography (ClinProt magnetic beads). In the first dimension serum specimen were fractionated according to the isoelectric point of protein components by free-flow electrophoresis (IEF-FFE). Subsequently, fractions were separated in a second dimension by ClinProt and protein profiling was done by MALDI-TOF analysis. Our investigation show that in contrast to ClinProt approach alone the combination of both techniques enhances detectable protein mass signals by a factor of fifteen coincided with high reproducibility (CV < 12% between different experiments). Therefore, we conclude that our combined approach improves the efficiency of MS based serum proteome analysis significantly.

From micro to macro: conversion of capillary electrophoretic separations of biomolecules and bioparticles to preparative free-flow electrophoresis scale

This invited contribution in the special issue of Electrophoresis published in celebration of the 30th Anniversary of this journal reflects the impact of our milestone paper [Prusík, Z., Kasicka, V., Mudra, P., Stepánek, J., Smékal, O., Hlavácek, J., Electrophoresis 1990, 11, 932-936] in the area of conversion of microscale analytical and micropreparative CE separations of biomolecules and bioparticles into (macro)preparative free-flow electrophoresis (FFE) scale on the basis of a correlation between CE and FFE methods. In addition to the survey of advances in the relatively narrow field of CE-FFE correlation and CE-FFE conversion, a comprehensive review of the recent developments of micropreparative CE and (macro)preparative FFE techniques is also presented and applications of these techniques to micro- and (macro)preparative separations and purifications of biomolecules and bioparticles are demonstrated. The review covers the period since the year of publication of the above paper, i.e. ca. the last 20 years.

Functional and complementary phosphorylation state attributes of human insulin-like growth factor-binding protein-1 (IGFBP-1) isoforms resolved by free flow electrophoresis

Fetal growth restriction (FGR) is a common disorder in which a fetus is unable to achieve its genetically determined potential size. High concentrations of insulin-like growth factor-binding protein-1 (IGFBP-1) have been associated with FGR. Phosphorylation of IGFBP-1 is a mechanism by which insulin-like growth factor-I (IGF-I) bioavailability can be modulated in FGR. In this study a novel strategy was designed to determine a link between IGF-I affinity and the concomitant phosphorylation state characteristics of IGFBP-1 phosphoisoforms. Using free flow electrophoresis (FFE), multiple IGFBP-1 phosphoisoforms in amniotic fluid were resolved within pH 4.43-5.09. The binding of IGFBP-1 for IGF-I in each FFE fraction was determined with BIAcore biosensor analysis. The IGF-I affinity (K(D)) for different IGFBP-1 isoforms ranged between 1.12e-08 and 4.59e-07. LC-MS/MS characterization revealed four phosphorylation sites, Ser(P)(98), Ser(P)(101), Ser(P)(119), and Ser(P)(169), of which Ser(P)(98) was new. Although the IGF-I binding affinity for IGFBP-1 phosphoisoforms across the FFE fractions did not correlate with phosphopeptide intensities for Ser(P)(101), Ser(P)(98), and Ser(P)(169) sites, a clear association was recorded with Ser(P)(119). Our data demonstrate that phosphorylation at Ser(119) plays a significant role in modulating affinity of IGFBP-1 for IGF-I. In addition, an altered profile of IGFBP-1 phosphoisoforms was revealed between FGR and healthy pregnancies that may result from potential site-specific phosphorylation. This study provides a strong basis for use of this novel approach in establishing the linkage between phosphorylation of IGFBP-1 and FGR. This overall strategy will also be broadly applicable to other phosphoproteins with clinical and functional significance.

Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis

Due to ease of accessibility, plasma has become the sample of choice for proteomics studies directed towards biomarker discovery intended for use in diagnostics, prognostics and even in theranostics. The result of these extensive efforts is a long list of potential biomarkers, very few of which have led to clinical utility. Why have so many potential biomarkers failed validation? Herein, we address certain issues encountered, which complicate biomarker discovery efforts originating from plasma. The advantages of stabilizing the sample at collection by the addition of protease inhibitors are discussed. The principles of free-flow electrophoresis (FFE) separation are provided together with examples applying to various studies. Finally, particular attention is given to plasma or serum analysis using multidimensional separation strategies into which the FFE is incorporated. The advantages of using FFE separation in these workflows are discussed.

Multidimensional liquid phase separations for mass spectrometry

Large part of the current research in biology, medicine, and biotechnology depends on the analysis of DNA (genomics), proteins (proteomics), or metabolites (metabolomics). The advances in biotechnology also command development of adequate analytical instrumentation capable to analyze minute amounts of samples. The analysis of the content of single cells may serve as an example of ultimate analytical applications. Most of the separation techniques have been developed in the last three decades and alternative approaches are being investigated. At present, the main protocols for analyses of complex mixtures include 2-DE (IEF) followed by electrophoresis in SDS polyacrylamide gel (SDS-PAGE) and chromatographic techniques. Information-rich techniques such as MS and NMR are essential for the identification and structure analysis of the analyzed compounds. High resolution separation of the individual sample components is often a prerequisite for success. High resolution proteomic analysis in the majority of laboratories still relies on the time consuming and laborious offline methods. This review highlights some of the important aspects of 2-D separations including microfluidics.

Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis

Blood plasma is the most complex human-derived proteome, containing other tissue proteomes as subsets. This proteome has only been partially characterized due to the extremely wide dynamic range of the plasma proteins of more than ten orders of magnitude. Thus, the reduction in sample complexity prior to mass spectrometric analysis is particularly important and alternative separation methodologies are required to more effectively mine the lower abundant plasma proteins. Here, we demonstrated a novel separation approach using 2-D free-flow electrophoresis (FFE) separating proteins and peptides in solution according to their pI prior to LC-MS/MS. We used the combination of sequential protein and peptide separation by first separating the plasma proteins into specific FFE fractions. Tryptic digests of the separated proteins were generated and subsequently separated using FFE. The protein separation medium was optimized to segregate albumin into specific fractions containing only few other proteins. An optimization of throughput for the protein separation reduced the separation time of 1 mL of plasma to approximately 3 h providing sufficient material for digestion and the subsequent peptide separation. Our approach revealed low-abundant proteins (e.g., L-selectin at 17 ng/mL and vascular endothelial-cadherin precursor at 30 ng/mL) and several tissue leakage products, thus providing a powerful orthogonal separation step in the proteomics workflow.

Free-flow electrophoresis of the human urinary proteome

Prefractionation of complex protein samples prior to mass spectrometry provides a method for the isolation of low-abundance proteins into specific fractions thereby enabling their identification. Free-flow electrophoresis in the isoelectric focusing mode (IEF-FFE) presents a complementary approach to established prefractionation methodologies. Proteins are separated in solution according to their isoelectric point (pI) with a high throughput of sample volume. The separation may be performed under denaturing or nondenaturing conditions and detergents may be added to promote protein solubilization. A protocol covering the pH range from pH 3 to 9 under denaturing conditions was used to illustrate the method of IEF-FFE including sample preparation prior to reversed-phase liquid chromatography and tandem mass spectrometry. The IEF-FFE separation was applied to a sample of human urine.

Recent developments in CE and CEC of peptides

The article brings a comprehensive survey of recent developments and applications of high-performance capillary electromigration methods, zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography, to analysis, preparation, and physicochemical characterization of peptides. New approaches to the theoretical description and experimental verification of electromigration behavior of peptides and to methodology of their separations, such as sample preparation, adsorption suppression, and detection, are presented. Novel developments in individual CE and CEC modes are shown and several types of their applications 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 CE and CEC techniques to provide important physicochemical characteristics of peptides are demonstrated.

Fishing for anti-leishmania drugs: principles and problems

To date, there are no vaccines against any of the major parasitic diseases including leishmaniasis, and chemotherapy is the main weapon in our arsenal. Current drugs are toxic and expensive, and are losing their effectiveness due to parasite resistance. The availability of the genome sequence of two species of Leishmania, Leishmania major and Leishmania infantum, as well as that of Trypanosoma brucei and Trypanosoma cruzi should provide a cornucopia of potential new drug targets. Their exploitation will require a multi-disciplinary approach that includes protein structure and function and high throughput screening of random and directed chemical libraries, followed by in vivo testing in animals and humans. We outline the opportunities that are made possible by recent technologies, and potential problems that need to be overcome.

Heparin chromatography to deplete high-abundance proteins for serum proteomics

BACKGROUND

Serum is a very informative sample for disease diagnosis. However, a few of the high-abundance proteins existing in serum make the identification of disease-specific serum biomarkers extremely challenging using currently available technologies. A highly promising first step for most analytical approaches of serum is to deplete as many of the high-abundance proteins as possible.

METHODS

We introduced the traditional method of heparin chromatography coupled with protein G sepharose to deplete the high-abundance proteins for serum proteomics.

RESULTS

Compared with the multiple affinity removal system (MARS) column (a commercial version to deplete 6 major proteins in serum), heparin chromatography can deplete more high-abundance proteins in a single step, especially many high molecular-weight proteins. Using this simple and inexpensive method to pretreat serum for 2-DE analysis, more protein spots can be visualized. IgGs depletion by protein G sepharose can further enhance the resolution of the resulting serum proteome.

CONCLUSIONS

Heparin chromatography coupled with protein G appears to be an efficient and economical strategy to pretreat serum for serum proteomics.

Sample preparation

A panorama of sample preparation methods has been composed from 481 references, with a highlight of some promising methods fast developed during recent years and a somewhat brief introduction on most of the well-developed methods. All the samples were commonly referred to molecular composition, being extendable to particles including cells but not to organs, tissues and larger bodies. Some criteria to evaluate or validate a sample preparation method were proposed for reference. Strategy for integration of several methods to prepare complicated protein samples for proteomic studies was illustrated and discussed.

Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution

Biomarker discovery produces lists of candidate markers whose presence and level must be subsequently verified in serum or plasma. Verification represents a paradigm shift from unbiased discovery approaches to targeted, hypothesis-driven methods and relies upon specific, quantitative assays optimized for the selective detection of target proteins. Many protein biomarkers of clinical currency are present at or below the nanogram/milliliter range in plasma and have been inaccessible to date by MS-based methods. Using multiple reaction monitoring coupled with stable isotope dilution mass spectrometry, we describe here the development of quantitative, multiplexed assays for six proteins in plasma that achieve limits of quantitation in the 1-10 ng/ml range with percent coefficients of variation from 3 to 15% without immunoaffinity enrichment of either proteins or peptides. Sample processing methods with sufficient throughput, recovery, and reproducibility to enable robust detection and quantitation of candidate biomarker proteins were developed and optimized by addition of exogenous proteins to immunoaffinity depleted plasma from a healthy donor. Quantitative multiple reaction monitoring assays were designed and optimized for signature peptides derived from the test proteins. Based upon calibration curves using known concentrations of spiked protein in plasma, we determined that each target protein had at least one signature peptide with a limit of quantitation in the 1-10 ng/ml range and linearity typically over 2 orders of magnitude in the measurement range of interest. Limits of detection were frequently in the high picogram/milliliter range. These levels of assay performance represent up to a 1000-fold improvement compared with direct analysis of proteins in plasma by MS and were achieved by simple, robust sample processing involving abundant protein depletion and minimal fractionation by strong cation exchange chromatography at the peptide level prior to LC-multiple reaction monitoring/MS. The methods presented here provide a solid basis for developing quantitative MS-based assays of low level proteins in blood.

Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis

The routine detection of low abundance components in complex samples for detailed proteomics analysis continues to be a challenge. Whilst the potential of multidimensional chromatographic fractionation for this purpose has been proposed for some years, and was used effectively for the purification to homogeneity of trace components in bulk biological samples for N-terminal sequence analysis, its practical application in the proteomics arena is still limited. This article reviews some of the recent data using these approaches, including the use of microaffinity purification as part of multidimensional protocols for downstream proteomics analysis.

Body fluid proteomics: Prospects for biomarker discovery

Many diseases are caused by perturbations of cellular signaling pathways and related pathway networks as a result of genetic aberrations. These perturbations are manifested by altered cellular protein profiles in the fluids bathing tissue/organs (i.e., the tissue interstitial fluid, TIF). A major challenge of clinical chemistry is to quantitatively map these perturbed protein profiles - the so-called "signatures of disease" - using modern proteomic technologies. This information can be utilized to design protein biomarkers for the early detection of disease, monitoring disease progression and efficacy of drug action. Here, we discuss the use of body fluids in the context of prospective biomarker discovery, and the marked 1000-1500-fold dilution of body fluid proteins, during their passage from TIF to the circulatory system. Further, we discuss proteomics strategies aimed at depleting major serum proteins, especially albumin, in order to focus on low-abundance protein/peptides in plasma. A major limitation of depletion strategies is the removal of low-molecular weight protein/peptides which specifically bind major plasma proteins. We present a prototype model, using albumin, for understanding the multifaceted nature of biomarker research, highlighting the involvement of albumin in Alzheimer's disease. This model underscores the need for a system-level understanding for biomarker research and personalized medicine.

Methods for samples preparation in proteomic research

Sample preparation is one of the most crucial processes in proteomics research. The results of the experiment depend on the condition of the starting material. Therefore, the proper experimental model and careful sample preparation is vital to obtain significant and trustworthy results, particularly in comparative proteomics, where we are usually looking for minor differences between experimental-, and control samples. In this review we discuss problems associated with general strategies of samples preparation, and experimental demands for these processes.

Biomarker discovery from body fluids using mass spectrometry

Systems analysis of body fluids by mass spectrometry (MS) is an upcoming field of biomarker research. This approach is extremely attractive because it does not require biomarker candidates and the sample preparation is simple. However, during the development of the technique strong critical comments were made on the poor reproducibility, the special characteristics of blood as a source of peptides and on the frequent non-adequate statistical analysis of the data. Here we discuss the efforts made in the last few years to develop suitable protocols, which could lead to biomarker discovery from body fluids by mass spectrometry. Our review focuses on the systems analysis of non-digested blood serum or plasma samples by MALDI-TOF and SELDI-TOF.

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer

We investigated the aberrant expression of plasma proteins in patients with pancreatic cancer. High-abundance plasma proteins (albumin, transferrin, haptoglobin, alpha-1-antitrypsin, IgG and IgA) were depleted by use of an immuno-affinity column, and low-abundance ones were separated into five fractions by anion-exchange chromatography. The fractionated plasma proteins were subjected to 2D-DIGE with highly sensitive fluorescent dyes. The quantitative protein expression profiles obtained by 2D-DIGE were compared between two plasma protein mixtures: one from five non-cancer bearing healthy donors and the other from five patients with pancreatic cancer. Among 1200 protein spots, we found that 33 protein spots were differently expressed between the two mixtures; 27 of these were up-regulated and six were down-regulated in cancer. Mass spectrometry and database searching allowed the identification of the proteins corresponding to the gel spots. Up-regulation of leucine-rich alpha-2-glycoprotein (LRG), which has not previously been implicated in pancreatic cancer, was observed. Western blotting with an anti-LRG antibody validated the up-regulation of LRG in an independent series of plasma samples from healthy controls, patients with chronic pancreatitis, and patients with pancreatic cancer. Our results demonstrate the application of a combination of multi-dimensional liquid chromatography with 2D-DIGE for plasma proteomics and suggest the clinical utility of LRG plasma level measurement.

Electrophoretic separations of cerebrospinal fluid proteins in clinical investigations

The cerebrospinal fluid (CSF) is a key sample in the research for novel molecular biomarkers of neurodegenerative disorders. CSF represents a repertoire of neuro-secreted, biosynthesised and metabolised molecular products of the central nervous system (CNS). Diffusion of macromolecules from the peripheral circulatory system to the CSF is highly regulated by the blood-brain barrier, which prevents uncontrolled distribution of proteins in the CNS. The development of reproducible high resolution separations of proteins in 2-D electrophoresis methods by the advent of immobilised pH gradient has opened the route to multivariate holistic protein pattern investigation of CSF into neurodegenerative disorders. Moreover, the introduction of pre-fractionation techniques such as free flow electrophoresis is currently increasing the dynamic depth of proteome analysis. Alzheimer's disease (AD) and other forms of dementia, demyelinating diseases, Parkinson's disease (PD), and Creutzfeldt-Jakob disease (CJD) have been evaluated for biomarker discovery by CSF investigation in multiple studies. However, the statistical design of these clinical cross-sectional investigations remains a limited factor given the strong statistical power required for complex multivariate analysis. These initial evidences are of particular interest in dissecting specific molecular mechanisms. The development of fast and economic profiling of CSF by linear matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) is providing a new ancillary technology to assess sample quality and pre-analytical requirements. In the following we take into account all these issues in the CSF proteomics investigation, especially highlighting the possible application in the development of clinical molecular biomarkers.

Clin Chem Lab Med 2007;45:437–49.

Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications

Recent advances in proteomics technologies provide tremendous opportunities for biomarker-related clinical applications; however, the distinctive characteristics of human biofluids such as the high dynamic range in protein abundances and extreme complexity of the proteomes present tremendous challenges. In this review we summarize recent advances in LC-MS-based proteomics profiling and its applications in clinical proteomics as well as discuss the major challenges associated with implementing these technologies for more effective candidate biomarker discovery. Developments in immunoaffinity depletion and various fractionation approaches in combination with substantial improvements in LC-MS platforms have enabled the plasma proteome to be profiled with considerably greater dynamic range of coverage, allowing many proteins at low ng/ml levels to be confidently identified. Despite these significant advances and efforts, major challenges associated with the dynamic range of measurements and extent of proteome coverage, confidence of peptide/protein identifications, quantitation accuracy, analysis throughput, and the robustness of present instrumentation must be addressed before a proteomics profiling platform suitable for efficient clinical applications can be routinely implemented.

Chipping into the human genome: novel insights for transplantation

High throughput, high density platforms for transcriptional, proteomic, and metabonomic analyses are opening new doors for improving our understanding of the complexity and redundancy of the immune system in the interplay of the innate and allo-immune responses in organ transplantation. New insights are being obtained into the possible discrepancies between the gold standard of tissue pathological diagnosis and clinical graft outcomes, as new transcriptional categories of transplant rejection evolve. The bystander effects of chronic immunosuppression underlying the complexities of graft dysfunction are beginning to be understood. Non-invasive mechanisms to monitor transplants, by following 'footprints' of biomarker sets that reflect the disease phenotype, are being pursued for their clinical application for direct patient care. Utilization of these same biomarker sets may also offer a unique means to titrate immunosuppression and predict specific graft dysfunction events prior to clinical decline, thus bringing in the potential to reduce patient morbidity from infection and malignancy, preserve graft integrity, and limit the progression of chronic graft injury. Bioinformatics support is integral to the unraveling of the mysteries of the human genome, proteome, and metabolome in disease and in health.

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.