Modern strategies for protein quantification in proteome analysis: advantages and limitations

Recent advances in the detection of glioblastoma, from imaging-based methods to proteomics and biosensors: A narrative review

Glioblastoma (GBM) is an aggressive type of cancer that originates in the cells called astrocytes, which support the functioning of nerve cells. It can develop in either the brain or the spinal cord and is also known as glioblastoma multiform. GBM is a highly aggressive cancer that can occur in either the brain or spinal cord. The detection of GBM in biofluids offers potential advantages over current methods for diagnosing and treatment monitoring of glial tumors. Biofluid-based detection of GBM focuses on identifying tumor-specific biomarkers in blood and cerebrospinal fluid. To date, different methods have been used to detect biomarkers of GBM, ranging from various imaging techniques to molecular approaches. Each method has its own strengths and weaknesses. The present review aims to scrutinize multiple diagnostic methods for GBM, with a focus on proteomics methods and biosensors. In other words, this study aims to provide an overview of the most significant research findings based on proteomics and biosensors for the diagnosis of GBM.

Protein Quantification and Imaging by Surface-Enhanced Raman Spectroscopy and Similarity Analysis

Protein quantification techniques such as immunoassays have been improved considerably, but they have several limitations, including time-consuming procedures, low sensitivity, and extrinsic detection. Because direct surface-enhanced Raman spectroscopy (SERS) can detect intrinsic signals of proteins, it can be used as an effective detection method. However, owing to the complexity and reliability of SERS signals, SERS is rarely adopted for quantification without a purified target protein. This study reports an efficient and effective direct SERS-based immunoassay (SERSIA) technique for protein quantification and imaging. SERSIA relies on the uniform coating of gold nanoparticles (GNPs) on a target-protein-immobilized substrate by simple centrifugation. As centrifugation induces close contact between the GNPs and target proteins, the intrinsic signals of the target protein can be detected. For quantification, the protein levels in a cell lysate are estimated using similarity analysis between antibody-only and protein-conjugated samples. This method reliably estimates the protein level at a sub-picomolar detection limit. Furthermore, this method enables quantitative imaging of immobilized protein at a micrometer range. Because this technique is fast, sensitive, and requires only one type of antibody, this approach can be a useful method to detect proteins in biological samples.

Transcriptomic and Proteomic Analysis of the Tentacles and Mucus of Anthopleura dowii Verrill, 1869

Sea anemone venom contains a complex and diverse arsenal of peptides and proteins of pharmacological and biotechnological interest, however, only venom from a few species has been explored from a global perspective to date. In the present study, we identified the polypeptides present in the venom of the sea anemone Anthopleura dowii Verrill, 1869 through a transcriptomic and proteomic analysis of the tentacles and the proteomic profile of the secreted mucus. In our transcriptomic results, we identified 261 polypeptides related to or predicted to be secreted in the venom, including proteases, neurotoxins that could act as either potassium (K⁺) or sodium (Na⁺) channels inhibitors, protease inhibitors, phospholipases A2, and other polypeptides. Our proteomic data allowed the identification of 156 polypeptides—48 exclusively identified in the mucus, 20 in the tentacles, and 88 in both protein samples. Only 23 polypeptides identified by tandem mass spectrometry (MS/MS) were related to the venom and 21 exclusively identified in the mucus, most corresponding to neurotoxins and hydrolases. Our data contribute to the knowledge of evolutionary and venomic analyses of cnidarians, particularly of sea anemones.

Quantitative profiling of CD13 on single acute myeloid leukemia cells by super-resolution imaging and its implication in targeted drug susceptibility assessment

Quantitative profiling of membrane proteins on the cell surface is of great interest in tumor targeted therapy and single cell biology. However, the existing technologies are either of insufficient resolution, or unable to provide precise information on the localization of individual proteins. Here, we report a new method that combines the use of quantum dot labeling, super-resolution microscopy (structured illumination microscopy, SIM) and software modeling. In this proof-of-principle study, we assessed the biological effects of Bestatin on individual cells from different AML cell lines expressing CD13 proteins, a potential target for tumor targeted therapy. Using the proposed method, we found that the different AML cell lines exhibit different CD13 expression densities, ranging from 0.1 to 1.3 molecules per μm2 cell surface, respectively. Importantly, Bestatin treatment assays shows that its effects on cell growth inhibition, apoptosis and cell cycle change are directly proportional to the density of CD13 on the cell surface of these cell lines. The results suggest that the proposed method advances the quantitative analysis of single cell surface proteins, and that the quantitative profiling information of the target protein on single cells has potential value in targeted drug susceptibility assessment.

Terminology of bioanalytical methods (IUPAC Recommendations 2018)

Recommendations are given concerning the terminology of methods of bioanalytical chemistry. With respect to dynamic development particularly in the analysis and investigation of biomacromolecules, terms related to bioanalytical samples, enzymatic methods, immunoanalytical methods, methods used in genomics and nucleic acid analysis, proteomics, metabolomics, glycomics, lipidomics, and biomolecules interaction studies are introduced.

DEEPN as an Approach for Batch Processing of Yeast 2-Hybrid Interactions

We adapted the yeast 2-hybrid assay to simultaneously uncover multiple transient protein interactions within a single screen by using a strategy termed DEEPN (dynamic enrichment for evaluation of protein networks). This approach incorporates high-throughput DNA sequencing and computation to follow competition among a plasmid population encoding interacting partners. To demonstrate the capacity of DEEPN, we identify a wide range of ubiquitin-binding proteins, including interactors that we verify biochemically. To demonstrate the specificity of DEEPN, we show that DEEPN allows simultaneous comparison of candidate interactors across multiple bait proteins, allowing differential interactions to be identified. This feature was used to identify interactors that distinguish between GTP- and GDP-bound conformations of Rab5.

A single step protein assay that is both detergent and reducer compatible: The cydex blue assay

Determination of protein concentration is often an absolute prerequisite in preparing samples for biochemical and proteomic analyses. However, current protein assay methods are not compatible with both reducers and detergents, which are however present simultaneously in most denaturing extraction buffers used in proteomics and electrophoresis, and in particular in SDS electrophoresis. It was found that inclusion of cyclodextrins in a Coomassie blue-based assay made it compatible with detergents, as cyclodextrins complex detergents in a 1:1 molecular ratio. As this type of assay is intrinsically resistant to reducers, a single-step assay that is both detergent and reducer compatible was developed. Depending on the type and concentration of detergents present in the sample buffer, either beta-cyclodextrin or alpha-cyclodextrin can be used, the former being able to complex a wider range of detergents and the latter being able to complex higher amounts of detergents due to its greater solubility in water. Cyclodextrins are used at final concentrations of 2-10 mg/mL in the assay mix. This typically allows to measure samples containing as little as 0.1 mg/mL protein, in the presence of up to 2% detergent and reducers such as 5% mercaptoethanol or 50 mM DTT in a single step with a simple spectrophotometric assay.

Methods and applications of absolute protein quantification in microbial systems

In the last years the scientific community faced an increased need to provide high-quality data on the concentration of single proteins within a cell. Especially against the background of the fast evolving field of systems biology this does not only apply for a few proteins but preferably for the whole proteome of the organism. Therefore there has been a rapid development from pure identification of proteins via characterization of changes between different conditions by relative protein quantification towards determination of absolute protein amounts for hundreds of protein species in a cell. This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail. The presented advantages and limitations of various methods may provide interested researchers help to appraise available methods, select the most appropriate technique and avoid common pitfalls during determination of protein concentration in a complex sample.

Spatially marking and quantitatively counting membrane immunoglobulin M in live cells via Ag cluster-aptamer probes

A probe composed of an aptamer and a silver cluster, where the aptamer targets mIgM of live cells and the silver cluster provides fluorescent imaging and mass quantification of mIgM of live cells, is presented. This new probe simultaneously provides accurate spatial and mass information of mIgM in live cells.

Inductively coupled plasma mass spectrometry-based immunoassay: a review

The last 10 years witnessed the emerging and growing up of inductively coupled plasma mass spectrometry (ICPMS)-based immunoassay. Its high sensitivity and multiplex potential have made ICPMS a revolutionary technique for bioanalyte quantification after element-tagged immunoassay. This review focuses on the major developments and the applications of ICPMS-based immunoassay, with emphasis on methodological innovations. The ICPMS-based immunoassay with elemental tags of metal ions, nanoparticles, and metal containing polymers was discussed in detail. The recent development of multiplex assay, mass cytometry, suspension array, and surface analysis demonstrated the versatility and great potential of this technique. ICPMS-based immunoassay has become one of the key methods in bioanalysis.

Targeted liquid chromatography quadrupole ion trap mass spectrometry analysis of tachykinin related peptides reveals significant expression differences in a rat model of neuropathic pain

Animal models are widely used to perform basic scientific research in pain. The rodent chronic constriction injury (CCI) model is widely used to study neuropathic pain. Animals were tested prior and after CCI surgery using behavioral tests (von Frey filaments and Hargreaves test) to evaluate pain. The brain and the lumbar enlargement of the spinal cord were collected from neuropathic and normal animals. Tachykinin related peptides were analyzed by high performance liquid chromatography quadrupole ion trap mass spectrometry. Our results reveal that the β-tachykinin₅₈₋₇₁, SP and SP₃₋₁₁ up-regulation are closely related to pain behavior. The spinal β-tachykinin₅₈₋₇₁, SP and SP₃₋₁₁ concentrations were significantly up-regulated in neuropathic animals compared with normal animals (p<0.001; p<0.001 and p<0.05, respectively). In contrast, the spinal SP5₅₋₁₁ concentration in neuropathic animals revealed a significant down-regulation compared with normal animals (p<0.05). The brain β-tachykinin₅₈₋₇₁ and SP concentrations were significantly up-regulated (p<0.05 and p<0.001, respectively). Interestingly, no significant concentration differences were observed in the spinal cord and brain for NKA, β-tachykinin₅₈₋₇₁, SP₁₋₇ and SP₆₋₁₁ (p>0.05). The β-tachykinin₅₈₋₇₁, SP and C-terminal SP metabolites could potentially serve as biomarkers in early drug discovery.

Peptide peak intensities enhanced by cysteine modifiers and MALDI TOF MS

Two cysteine-specific modifiers we reported previously, N-ethyl maleimide (NEM) and iodoacetanilide (IAA), have been applied to the labeling of cysteine residues of peptides for the purpose of examining the enhancement of ionization efficiencies in combination with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). The peak intensities of the peptides as a result of modification with these modifiers were compared with the peak intensities of peptides modified with a commercially available cysteine-specific modifier, iodoacetamide (IA). Our experiments show significant enhancement in the peak intensities of three cysteine-containing synthetic peptides modified with IAA compared to those modified with IA. The results showed a 4.5-6-fold increase as a result of modification with IAA compared to modification with IA. Furthermore, it was found that IAA modification also significantly enhanced the peak intensities of many peptides of a commercially available proteins, bovine serum albumin (BSA), compared to those modified with IA. This significant enhancement helped identify a greater number of peptides of these proteins, leading to a higher sequence coverage with greater confidence scores in identification of proteins with the use of IAA.

Leveraging proteomics to understand plant-microbe interactions

Understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. Proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. The various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. In this review, we discuss how these techniques have been applied to the study of plant-microbe interactions. We also present some areas where this field of study would benefit from the utilization of newly developed methods that overcome previous limitations. Finally, we reinforce the need for expanding, integrating, and curating protein databases, as well as the benefits of combining protein-level datasets with those from genetic analyses and other high-throughput large-scale approaches for a systems-level view of plant-microbe interactions.

Unraveling plant responses to bacterial pathogens through proteomics

Plant pathogenic bacteria cause diseases in important crops and seriously and negatively impact agricultural production. Therefore, an understanding of the mechanisms by which plants resist bacterial infection at the stage of the basal immune response or mount a successful specific R-dependent defense response is crucial since a better understanding of the biochemical and cellular mechanisms underlying these interactions will enable molecular and transgenic approaches to crops with increased biotic resistance. In recent years, proteomics has been used to gain in-depth understanding of many aspects of the host defense against pathogens and has allowed monitoring differences in abundance of proteins as well as posttranscriptional and posttranslational processes, protein activation/inactivation, and turnover. Proteomics also offers a window to study protein trafficking and routes of communication between organelles. Here, we summarize and discuss current progress in proteomics of the basal and specific host defense responses elicited by bacterial pathogens.

A general protease digestion procedure for optimal protein sequence coverage and post-translational modifications analysis of recombinant glycoproteins: application to the characterization of human lysyl oxidase-like 2 glycosylation

Using recombinant DNA technology for expression of protein therapeutics is a maturing field of pharmaceutical research and development. As recombinant proteins are increasingly utilized as biotherapeutics, improved methodologies ensuring the characterization of post-translational modifications (PTMs) are needed. Typically, proteins prepared for PTM analysis are proteolytically digested and analyzed by mass spectrometry. To ensure full coverage of the PTMs on a given protein, one must obtain complete sequence coverage of the protein, which is often quite challenging. The objective of the research described here is to design a protocol that maximizes protein sequence coverage and enables detection of post-translational modifications, specifically N-linked glycosylation. To achieve this objective, a highly efficient proteolytic digest protocol using trypsin was designed by comparing the relative merits of denaturing agents (urea and Rapigest SF), reducing agents [dithiothreitol (DTT) and tris(2-carboxyethyl)phophine (TCEP)], and various concentrations of alkylating agent [iodoacetamide (IAM)]. After analysis of human apo-transferrin using various protease digestion protocols, ideal conditions were determined to contain 6 M urea for denaturation, 5 mM TCEP for reduction, 10 mM IAM for alkylation, and 10 mM DTT, to quench excess IAM before the addition of trypsin. This method was successfully applied to a novel recombinant protein, human lysyl oxidase-like 2. Furthermore, the glycosylation PTMs were readily detected at two glycosylation sites in the protein. These digestion conditions were specifically designed for PTM analysis of recombinant proteins and biotherapeutics, and the work described herein fills an unmet need in the growing field of biopharmaceutical analysis.

Cysteine tagging for MS-based proteomics

Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.

Massively parallel concentration device for multiplexed immunoassays

A massively parallel nanofluidic concentration device array for multiplexed and high-throughput biomolecule detection is demonstrated. By optimizing the microchannel/nanojunction design and channel conductivity, an array of up to 128 nanofluidic concentration devices were fabricated. Operation of the entire array requires only one inlet and one outlet reservoir, with the application of a single operational voltage bias across them. Concentration efficiencies of the devices were found to be uniform within the array, within 5% error. Alternatively, concentration speed in each channel can be individually tuned by controlling the length of the inlet microchannel and thus controlling the flow rate based on change of the tangential electric field. This allows immuno-binding reactions at different concentration ranges to be performed in parallel. Using multiplexed, successive-concentration enhanced detection in the device, we have shown that the dynamic range and reliability of the immunoassay can be significantly increased.

Oxidative protein labeling in mass-spectrometry-based proteomics

Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)-mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.

The Sod2 mutant mouse as a model for oxidative stress: a functional proteomics perspective

Oxidative stress has been implicated in the pathogenesis of numerous human diseases and disorders, but the mechanistic basis often remains enigmatic. The Sod2 mutant mouse, which is sensitized to mitochondrial stress, is an ideal mutant model for studying the role of oxidative stress in a diverse range of complications arising from mitochondrial dysfunction and diminished antioxidant defense. To fully appreciate the widespread molecular consequences under increased oxidative stress, a systems approach utilizing proteomics is able to provide a global overview of the complex biological changes, which a targeted single biomolecular approach cannot address fully. This review focuses on the applications of mass spectrometry and functional proteomics in the Sod2 mouse. The combinatorial approach provides novel insights into the interplay of chemistry and biology, free radicals and proteins, thereby augmenting our understanding of how redox perturbations influence protein dynamics. Ultimately, this knowledge can lead to the development of free radical-targeted therapies.

Cysteine-reactive covalent capture tags for enrichment of cysteine-containing peptides

Considering the tremendous complexity and the wide dynamic range of protein samples from biological origin and their proteolytic peptide mixtures, proteomics largely requires simplification strategies. One common approach to reduce sample complexity is to target a particular amino acid in proteins or peptides, such as cysteine (Cys), with chemical tags in order to reduce the analysis to a subset of the whole proteome. The present work describes the synthesis and the use of two new cysteinyl tags, so-called cysteine-reactive covalent capture tags (C3T), for the isolation of Cys-containing peptides. These bifunctional molecules were specifically designed to react with cysteines through iodoacetyl and acryloyl moieties and permit efficient selection of the tagged peptides. To do so, a thioproline was chosen as the isolating group to form, after a deprotection/activation step, a thiazolidine with an aldehyde resin by the covalent capture (CC) method. The applicability of the enrichment strategy was demonstrated on small synthetic peptides as well as on peptides derived from digested proteins. Mass spectrometric (MS) analysis and tandem mass spectrometric (MS/MS) sequencing confirmed the efficient and straightforward selection of the cysteine-containing peptides. The combination of C3T and CC methods provides an effective alternative to reduce sample complexity and access low abundance proteins.

Evaluation of the ALiPHAT method for PC-IDMS and correlation of limits-of-detection with nonpolar surface area

PC-IDMS experiments for two peptides, laminin nonapeptide and the N-terminal tryptic peptide of prostate specific antigen, were performed utilizing a variety of alkylating reagents. These experiments were conducted to investigate how hydrophobicity influences the limits-of-detection (LOD) by altering their electrospray ionization response. Nonpolar surface areas were calculated for both peptides and all alkylating reagents to provide an estimate of the hydrophobicity of the differently alkylated peptides. Decreases in LOD by 2-fold were observed for both peptides between the best and worst performing combination of alkylating reagent. However, while an increase in hydrophobicity was found to aid in decreasing LOD to an extent, beyond a certain hydrophobicity, we observed a decrease.

Bayesian Analysis of iTRAQ Data with Nonrandom Missingness: Identification of Differentially Expressed Proteins

iTRAQ (isobaric Tags for Relative and Absolute Quantitation) is a technique that allows simultaneous quantitation of proteins in multiple samples. In this paper, we describe a Bayesian hierarchical model-based method to infer the relative protein expression levels and hence to identify differentially expressed proteins from iTRAQ data. Our model assumes that the measured peptide intensities are affected by both protein expression levels and peptide specific effects. The values of these two effects across experiments are modeled as random effects. The nonrandom missingness of peptide data is modeled with a logistic regression which relates the missingness probability for a peptide with the expression level of the protein that produces this peptide. We propose a Markov chain Monte Carlo method for the inference of model parameters, including the relative expression levels across samples. Our simulation results suggest that the estimates of relative protein expression levels based on the MCMC samples have smaller bias than those estimated from ANOVA models or fold changes. We apply our method to an iTRAQ dataset studying the roles of Caveolae for postnatal cardiovascular function.

Protein turnover in mycobacterial proteomics

Understanding the biology of Mycobacterium tuberculosis is one of the primary challenges in current tuberculosis research. Investigation of mycobacterial biology using the systems biology approach has deciphered much information with regard to the bacilli and tuberculosis pathogenesis. The modulation of its environment and the ability to enter a dormant phase are the hallmarks of M. tuberculosis. Until now, proteome studies have been able to understand much about the role of various proteins, mostly in growing M. tuberculosis cells. It has been difficult to study dormant M. tuberculosis by conventional proteomic techniques with very few proteins being found to be differentially expressed. Discrepancy between proteome and transcriptome studies lead to the conclusion that a certain aspect of the mycobacterial proteome is not being explored. Analysis of protein turnover may be the answer to this dilemma. This review, while giving a gist of the proteome response of mycobacteria to various stresses, analyzes the data obtained from abundance studies versus data from protein turnover studies in M. tuberculosis. This review brings forth the point that protein turnover analysis is capable of discerning more subtle changes in protein synthesis, degradation, and secretion activities. Thus, turnover studies could be incorporated to provide a more in-depth view into the proteome, especially in dormant or persistent cells. Turnover analysis might prove helpful in drug discovery and a better understanding of the dynamic nature of the proteome of mycobacteria.

Synergistic design of electric field and membrane in facilitating continuous adsorption for cleanup and enrichment of proteins in direct ESI-MS analysis

We designed and fabricated a novel microdevice to facilitate continuous adsorption phenomena for biological sample preparation. Using the device, we also developed an online, highly integrated, multifunctional strategy, with a promise of accepting a large volume of crude tissue extracts with the end point generation of a reliable MS identification within 20 min. Under an external electric field, charged membranes can adsorb multiple layers of proteins, which exceed the capacity limit of common resins or membranes. It enlarges sample loading and trapping efficiency, thus bypasses the tradeoff between sample capacity and downstream detection sensitivity. This integrated approach, formed by synergistic utilization among electric field, membrane, and fluidic handling at the microscale, reduces the overall complexity of crude samples in one step for direct MS analysis. The sample preparation goals, including enrichment, desalting, removal of noncharged contaminants, and initial fractionation, can be rapidly performed in a single device. The strategy facilitates reproducible MS quantification by circumventing traditional laborious and time-consuming sample preparation steps. In addition, MEPD extended the ion trap linear dynamic range from 2 to at least 4 orders of magnitude by eliminating ion suppression effect, enriching target analyte(s), and decreasing sample loss during integrated sample preparation.

Microfluidics with MALDI analysis for proteomics--a review

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

Isotope-coded two-dimensional maps: tagging with deuterated acrylamide and 2-vinylpyridine

Isotope-coded two-dimensional maps, with either D(0)/D(3)-acrylamide or D(0)/D(4) 2-vinyl pyridine, are described in detail. They have the advantage of running the two samples under investigation within a single slab gel, thus minimizing errors because of spot matching with software packages when samples are run in parallel maps. Labeling with deuterated acrylamide is very simple and inexpensive, because this chemical is commercially available. The experiment has to be carried out at alkaline pH values (pH 8.5-9.0) and with high molarities of alkylating agent (50-100 mM) to ensure good conversion efficiency. On the contrary, labeling with 2-vinyl pyridine (2-VP) can be performed in much lower alkylant molarities (20 mM) and at neutral pH values, thus ensuring essentially 100% conversion efficiency coupled with 100% specificity, because the reaction is sustained by the partial positive and negative charges on the 2-VP and -SH group, respectively. However, deuterated 2-VP is not commercially available and it has to be synthesized ad hoc.

Matrix-assisted laser desorption/ionization-MS-based relative quantification of peptides and proteins using iodoacetamide and N-methyliodoacetamide as labeling reagents

The use of iodoacetamide (IAA) and N-methyliodoacetamide (MIAA) as labeling agents for the relative measurements of proteins using MALDI-MS is described herein. These reagents, which alkylate the thiol groups of cysteine residues in proteins, were introduced during the alkylation step of a common protein denaturation and digestion process. This approach is simpler and cheaper than those involving isotope labeling agents. The labeling agents described herein displayed good dynamic ranges and correlation coefficients for protein quantification analyses when the proteins were treated through either in-solution or in-gel digestion. The best dynamic ranges (in the molar ratio) for proteins lysozyme, transferrin, and BSA (in-solution digestion) are 0.1-10, 0.1-8, and 0.1-8, respectively. The corresponding correlation coefficients are greater than 0.99. The IAA/MIAA labeling is a useful method for the relative quantification of peptides and digested proteins when the chromatographic isotope effect is not a major concern.

Biomarkers for lysosomal storage disorders: identification and application as exemplified by chitotriosidase in Gaucher disease

A biomarker is an analyte that indicates the presence of a biological process linked to the clinical manifestations and outcome of a particular disease. An ideal biomarker provides indirect but ongoing determinations of disease activity. In the case of lysosomal storage disorders (LSDs), metabolites or proteins specifically secreted by storage cells are good candidates for biomarkers. Potential clinical applications of biomarkers are found in improved diagnosis, monitoring of disease progression and assessment of therapeutic correction. These applications are illustrated by reviewing the use of plasma chitotriosidase in the clinical management of patients with Gaucher disease, the most common LSD. The ongoing debate on the value of biomarkers in patient management is addressed. Novel analytical methods have revolutionized the identification and measurement of biomarkers at the protein and metabolite level. Recent developments in biomarker discovery by proteomics are described and the future for biomarkers of LSDs is discussed.

CONCLUSION

Besides direct applications for biomarkers in patient management, biomarker searches are likely to render new insights into pathophysiological mechanisms and metabolic adaptations, and may provide new targets for therapeutic intervention.

Proteases for processing proneuropeptides into peptide neurotransmitters and hormones

Peptide neurotransmitters and peptide hormones, collectively known as neuropeptides, are required for cell-cell communication in neurotransmission and for regulation of endocrine functions. Neuropeptides are synthesized from protein precursors (termed proneuropeptides or prohormones) that require proteolytic processing primarily within secretory vesicles that store and secrete the mature neuropeptides to control target cellular and organ systems. This review describes interdisciplinary strategies that have elucidated two primary protease pathways for prohormone processing consisting of the cysteine protease pathway mediated by secretory vesicle cathepsin L and the well-known subtilisin-like proprotein convertase pathway that together support neuropeptide biosynthesis. Importantly, this review discusses important areas of current and future biomedical neuropeptide research with respect to biological regulation, inhibitors, structural features of proneuropeptide and protease interactions, and peptidomics combined with proteomics for systems biological approaches. Future studies that gain in-depth understanding of protease mechanisms for generating active neuropeptides will be instrumental for translational research to develop pharmacological strategies for regulation of neuropeptide functions. Pharmacological applications for neuropeptide research may provide valuable therapeutics in health and disease.

Optimization of two-dimensional gel electrophoresis technique for liver fibrosis tissue from patients with hepatitis B

AIM: To establish and optimize the technique of two-dimensional gel electrophoresis (2-DE) for studying the proteomics of liver fibrosis tissue from patients with hepatitis B.

METHODS: Liver fibrosis tissues were obtained by surgical method, and the total proteins were extracted. Immobilized pH gradient isoelectric two-dimensional gel electrophoresis was used to separate the total protein. After coomassie brilliant blue staining, 2-DE maps were analyzed with ImageMaster 2D Platinum Software. A series of conditions such as the sample size, electrophoresis parameters and the way to treat the sample were improved.

RESULTS: After optimization, the horizontal trail was decreased; the resolution of the spot was improved; the number of protein spot was increased from 246 ± 33 to 729 ± 83 in the 2-DE maps.

CONCLUSION: The optimized technique of 2-DE can be introduced to study the proteomics of liver fibrosis tissue from patients with hepatitis B.

Achieving Augmented Limits of Detection for Peptides with Hydrophobic Alkyl Tags

The wide range of protein concentrations found in biological matrixes presents a formidable analytical challenge in proteomics experiments. It is predicted that low-abundance proteins are the likely clinically relevant targets in disease-based proteomics analyses. To effectively analyze low-abundance proteins by electrospray ionization mass spectrometry, limits of detection must be improved upon. Previous studies have demonstrated hydrophobicity is a main determinant of the electrospray ionization response. One would expect to improve the electrospray ionization response of a hydrophilic peptide by making it more hydrophobic, thus increasing the molecule's affinity for the surface of the electrospray droplet, thereby allowing the molecule to more effectively compete for charge. In this report, we demonstrate a strategy to increase the electrospray ionization response of cysteine-containing peptides with the addition of an octylcarboxyamidomethyl modification via alkylation chemistry, which we name the ALiPHAT strategy (augmented limits of detection for peptides with hydrophobic alkyl tags). We demonstrate the relative increase in electrospray ionization response of peptides with an octylcarboxyamidomethyl modification compared to carboxyamidomethyl-modified peptides upon LC-MS analysis. Furthermore, we show the octylcarboxyamidomethyl group does not fragment or undergo neutral loss during collision-induced dissociation. Collectively, our results demonstrate the feasibility of the octylcarboxyamidomethyl modification to improve limits of detection for cysteine-containing peptides.

Improvement of recovery and repeatability in liquid chromatography-mass spectrometry analysis of peptides

Poor repeatability of peak areas is a problem frequently encountered in peptide analysis with nanoLiquid Chromatography coupled on-line with Mass Spectrometry (nanoLC-MS). As a result, quantitative analysis will be seriously hampered unless the observed variability can be corrected in some way. Currently, labeling techniques or addition of internal standards are often applied for this purpose. However, these procedures are elaborate and error-prone and may render complex samples even more complex. Moreover, whenever poor repeatability results from variable recovery, not just quantification, but also sensitivity is affected. We have studied the parameters influencing the repeatability of chromatographic peak areas for a model set of proteolytic peptides (i.e., a cytochrome c tryptic digest) in nanoLC-MS analysis. It is demonstrated that repeatability issues are mainly due to poor recovery of peptides from the sample vial. Problems are largely resolved by addition of an organic modifier to the sample vial to improve solubility of the peptides, but care needs to be taken not to lose peptides due to reduced affinity for reversed-phase materials. Good results are obtained when applying dimethylsulfoxide (DMSO) for this purpose. When applying DMSO, repeatability increases, and the limit of detection (LOD) decreases. For the most hydrophobic peptides, a gain in LOD of at least an order of magnitude is obtained. In an aqueous sample containing 0.1% formic acid (FA), it is possible to detect 100-200 fmol of peptide, whereas +/-10 fmol can be detected in a sample containing 5% FA and 25% DMSO (10 microL injections).

Radical induced fragmentation of amino acid esters using triphenylcorrole(CuIII) complexes

A triphenylcorrole(CuIII) complex is covalently bound to amino acid esters at the nitrogen atom. As a result radical anions are generated, inducing the occurrence of side-chain reactions under CID conditions. Almost all of the amino acid esters that were studied show abundant ions that correspond to fragmentation at the alpha carbon either with or without the loss of the alkoxy ester moiety. Distinctive CID spectra were also recorded for leucine and isoleucine complexes. Initial results with short peptides are also shown.

Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF

A comparative study on the three quantitative methods frequently used in proteomics, 2D DIGE (difference gel electrophoresis), cICAT (cleavable isotope-coded affinity tags) and iTRAQ (isobaric tags for relative and absolute quantification), was carried out. DIGE and cICAT are familiar techniques used in gel- and LC-based quantitative proteomics, respectively. iTRAQ is a new LC-based technique which is gradually gaining in popularity. A systematic comparison among these quantitative methods has not been reported. In this study, we conducted well-designed comparisons using a six-protein mixture, a reconstituted protein mixture (BSA spiked into human plasma devoid of six abundant proteins), and complex HCT-116 cell lysates as the samples. All three techniques yielded quantitative results with reasonable accuracy when the six-protein or the reconstituted protein mixture was used. In DIGE, accurate quantification was sometimes compromised due to comigration or partial comigration of proteins. The iTRAQ method is more susceptible to errors in precursor ion isolation, which could be manifested with increasing sample complexity. The quantification sensitivity of each method was estimated by the number of peptides detected for each protein. In this regard, the global-tagging iTRAQ technique was more sensitive than the cysteine-specific cICAT method, which in turn was as sensitive as, if not more sensitive than, the DIGE technique. Protein profiling on HCT-116 and HCT-116 p53 -/- cell lysates displayed limited overlapping among proteins identified by the three methods, suggesting the complementary nature of these methods.

Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease

Novel approaches for the qualitative and quantitative proteomics analysis by nanoscale LC-MS applied to the study of protein expression response in depleted and undepleted serum of Gaucher patients undergoing enzyme replacement therapy are presented. Particular emphasis is given to the method reproducibility of these LC-MS experiments without the use of isotopic labels. The level of chitotriosidase, an established Gaucher biomarker, was assessed by means of an absolute concentration determination technique for alternate scanning LC-MS generated data. Disease associated proteins, including fibrinogens, complement cascade proteins, and members of the high density lipoprotein serum content, were recognized by various clustering methods and sorting and intensity profile grouping of identified peptides. Condition-unique LC-MS protein signatures could be generated utilizing the measured serum protein concentrations and are presented for all investigated conditions. The clustering results of the study were also used as input for gene ontology searches to determine the correlation between the molecular functions of the identified peptides and proteins.

LC/MS characterization of undesired products formed during iodoacetamide derivatization of sulfhydryl groups of peptides

Many undesired by-products have been noticed during alkylation with iodoacetamide, a widely used derivatization reaction in proteomics for the determination of sulfhydryl groups in peptides and proteins. We report here that iodoacetamide reacts with the N-terminal NH2 and the C-terminal carboxylic acid groups, in addition to the peripheral residues bearing protic functional groups. If sufficient reaction time is given, the N-terminal NH2 group is readily dialkylated by iodoacetamide. In fact, the N-terminal NH2 group reacts even faster than the reactive sites present in residues, such as tyrosine or histidine. LC/MS investigations with certain reactive peptides show that by-products are formed in a relatively short reaction time, even at room temperature. Interestingly, derivatives formed in this way are useful for sequence determination of peptides by MS since the intensities of y'' ions are highly suppressed in the spectra of N-terminus mono- and dialkylated peptides, whereas those of b-ions are significantly enhanced. For example, in the spectrum of N,N-dicarboxamidomethyl derivative of Val-Ala-Ala-Phe (VAAF), the y-series ions are virtually absent. On the other hand, when the derivatization takes place at the carboxylic group, the y-series ions are markedly observed in the spectra of these undesired O-carboxamidomethyl derivatives.

Precolumn derivatization of cysteine residues for quantitative analysis of five major cytochrome P450 isoenzymes by liquid chromatography/tandem mass spectrometry

The development of a novel method for absolute quantification of the five most clinically relevant CYP450 isoenzymes is described based on chemical derivatization of cysteine residues. The sulfhydryl-reactive reagents, 2-bromo-4'-chloroacetophenone (p-CPB) and 2-bromo-4'-bromoacetophenone (p-BPB), are proposed for use in quantitative proteomics. After reducing and denaturing, the P450s are derivatized with p-CPB for sulfhydryl alkylation then subjected to trypsin digestion. The resulting p-CPB-attached peptides are enriched using a phenyl resin solid-phase cartridge, then separated on a Zorbax 300SB reversed-phase column, and detected under positive electrospray ionization in the multiple reaction monitoring mode. Quantification is achieved using p-BPB-modified peptides as internal standards. Validation results demonstrated that this method showed good linearity between the concentration range of 10 fmol/microg to 5 pmol/microg for the six selected peptides in a complex matrix (rat liver microsomal protein). Intra-day and inter-day precision, expressed by relative standard deviation, were all less than 18%. Assay accuracy was within +/- 20% in terms of relative error. The quantitative derivatization approach proved to be reproducible, cost-effective and readily suitable for high-throughput assays. The reliability of this method for quantification of intact P450s was demonstrated through comparing with the well-applied isotope-coded affinity tag (ICAT) method.

An isotope coding strategy for proteomics involving both amine and carboxyl group labeling

A stable isotope coding strategy is described for the analysis of all types of tryptic peptides, including those that are N-terminally blocked and from the C-terminus of proteins. The method exploits differential derivatization of amine and carboxyl groups generated during proteolysis as a means of coding. Carboxyl groups produced during proteolysis incorporate 18O from H2(18)O. Peptides from the C-terminus of proteins were not labeled with 18O unless they contained a basic C-terminal amino acid. Primary amines form controls, and experimental samples were differentially acylated after proteolysis with either 1H3- or 2H3-N-acetoxysuccinamide. When these two types of labeling were combined, unique coding patterns were achieved for peptides arising from the C-termini and blocked N-termini of proteins.

Probiotic preparation has the capacity to hydrolyze proteins responsible for wheat allergy

This study was aimed at showing the capacity of probiotic VSL#3 to hydrolyze wheat flour allergens. Hydrolysis was investigated either by the use of baker's yeast bread treated with digestive enzymes and VSL#3, an experimental design that mimicked the activity of probiotics during gut colonization, or by the use of VSL#3 as a starter for dough fermentation, an experimental design that mimicked the predigestion of wheat flour proteins during food processing. Albumins, globulins, and gliadins extracted from wheat flour and chemically acidified and started dough and total proteins extracted from breads were analyzed by immunoblotting with pooled sera from patients with an allergy to wheat. Hydrolysis of wheat flour proteins was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2DE). Mass spectrometry matrix-assisted laser desorption and ionization-time of flight was used to identify some immunoglobulin E (IgE)-binding proteins. As shown by immunoblotting with sera from allergic patients, several IgE-binding proteins persisted after treatment of baker's yeast bread by pepsin and pancreatin. The signal of all these IgE-binding proteins disappeared after further treatment by VSL#3. As shown by SDS-PAGE and related immunoblotting and 2DE analyses, when VSL#3 was used as a starter for bread making, it caused a marked degradation of wheat proteins, including some IgE-binding proteins such as the putative transcription factor APFI and wheat alpha-amylase inhibitors. Indeed, the IgE-binding profile of the bread manufactured by VSL#3 was largely different from that of baker's yeast bread. The IgE-binding proteins that persisted in the bread made with VSL#3 were completely degraded by pepsin and pancreatin.