Use of hydrophilic interaction chromatography for the study of tyrosine protein kinase specificity

Targeted proteomics: a bridge between discovery and validation

New technologies in mass spectrometry are beginning to mature and show unique advantages for the identification and quantitation of proteins. In recent years, one of the significant goals of clinical proteomics has been to identify biomarkers that can be used for clinical diagnosis. As technology has progressed, the list of potential biomarkers has grown. However, the verification and validation of these potential biomarkers is increasingly challenging and require high-throughput quantitative assays, targeting specific candidates. Targeted proteomics bridges the gap between biomarker discovery and the development of clinically applicable biomarker assays.

A comprehensive workflow of mass spectrometry-based untargeted metabolomics in cancer metabolic biomarker discovery using human plasma and urine

Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC-LC), reversed-phase liquid chromatography (RP-LC), and gas chromatography (GC). All three techniques are coupled to a mass spectrometer (MS) in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM) and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow.

Systematic evaluation of acetone and acetonitrile for use in hydrophilic interaction liquid chromatography coupled with electrospray ionization mass spectrometry of basic small molecules

Sub-2-µm particle size hydrophilic interaction liquid chromatography [HILIC] combined with mass spectrometry has been increasing in popularity as a complementary technique to reversed-phase LC for the analysis of polar analytes. The organic-rich mobile phase associated with HILIC techniques provides increases in compound ionization, due to increased desolvation efficiency during electrospray ionisation mass spectrometric (ESI-MS) analysis. Although recent publications illustrated selectivity and response comparisons between reversed-phase LC/MS and HILIC LC/MS, there are limited discussions evaluating the optimisation of the mass spectrometry parameters regarding analytes and alternative mobile phases. The use of acetone as an alternative organic modifier in HILIC has been investigated with respect to signal-to-noise in ESI-MS for a variety of polar analytes. Analyte reponses were measured based on a variety of cone and capillary voltages at low and high pH in both acetone and acetonitrile. In order to visualise compound behaviour in the ESI source, surface plots were constructed to assist in interpreting the observed results. The use of acetone in ESI is complicated at low m/z due to the formation of condensation products. Favourable responses were observed for certain analytes and we envisage offering an insight into the use of acetone as an alternative to acetonitrile under certain analytical conditions for particular compound classifications for small molecule analysis. We also highlight the importance of optimising source voltages in order to obtain the maximum signal stability and sensitivity, which are invariably, highly solvent composition dependent parameters.

Quantitative liquid chromatography tandem mass spectrometry analysis of macromolecules using signature peptides in biological fluids

Targeted protein quantification using peptide surrogates has increasingly become important to the validation of biomarker candidates and development of protein therapeutics. These approaches have been proposed and employed as alternatives to immunoassays in biological fluids. Technological advances over the last 20 years in biochemistry and mass spectrometry have prompted the use of peptides as surrogates to quantify enzyme digested proteins using triple quadrupole mass spectrometers. Multiple sample preparation processes are often incorporated to achieve quantification of target proteins using these signature peptides. This review article focuses on these processes or hyphenated techniques for quantification of proteins with peptide surrogates. The most recent advances and strategies involved with hyphenated techniques are discussed.

Comprehensive mass spectrometry based metabolic profiling of blood plasma reveals potent discriminatory classifiers of pancreatic cancer

Poor outcome of pancreatic cancer necessitates development of an early diagnostic method to reduce mortality. No reliable early diagnostic test for pancreatic cancer detection has been developed and validated to date. In the current study, metabolic profiling of plasma samples from selected cancer patients and noncancerous controls was performed to seek novel metabolic biomarkers of pancreatic cancer. A comprehensive mass spectrometry based analytical platform established at the Metabolomics Core of the UC Davis Genome Center allowed detection of multiple compounds previously unreported in plasma from pancreatic cancer patients. It was found that selective amino acids, bile acids, and polar lipids were detected with increased or decreased levels in pancreatic cancer samples compared to controls. These findings on blood plasma levels of the relevant metabolites might be very useful clinical parameters for early diagnosis of pancreatic cancer.

Probing genetic algorithms for feature selection in comprehensive metabolic profiling approach

Six different clones of 1-year-old loblolly pine (Pinus taeda L.) seedlings grown under standardized conditions in a green house were used for sample preparation and further analysis. Three independent and complementary analytical techniques for metabolic profiling were applied in the present study: hydrophilic interaction chromatography (HILIC-LC/ESI-MS), reversed-phase liquid chromatography (RP-LC/ESI-MS), and gas chromatography all coupled to mass spectrometry (GC/TOF-MS). Unsupervised methods, such as principle component analysis (PCA) and clustering, and supervised methods, such as classification, were used for data mining. Genetic algorithms (GA), a multivariate approach, was probed for selection of the smallest subsets of potentially discriminative classifiers. From more than 2000 peaks found in total, small subsets were selected by GA as highly potential classifiers allowing discrimination among six investigated genotypes. Annotated GC/TOF-MS data allowed the generation of a small subset of identified metabolites. LC/ESI-MS data and small subsets require further annotation. The present study demonstrated that combination of comprehensive metabolic profiling and advanced data mining techniques provides a powerful metabolomic approach for biomarker discovery among small molecules. Utilizing GA for feature selection allowed the generation of small subsets of potent classifiers.

Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides

If an ion-exchange column is eluted with a predominantly organic mobile phase, then solutes can be retained through hydrophilic interaction even if they have the same charge as the stationary phase. This combination is termed electrostatic repulsion-hydrophilic interaction chromatography (ERLIC). With mixtures of solutes that differ greatly in charge, repulsion effects can be exploited to selectively antagonize the retention of the solutes that normally would be the best retained. This permits the isocratic resolution of mixtures that normally require gradients, including peptides, amino acids, and nucleotides. ERLIC affords convenient separations of highly charged peptides that cannot readily be resolved by other means. In addition, phosphopeptides can be isolated selectively from a tryptic digest.

Hydrophilic interaction chromatography

Separation of polar compounds on polar stationary phases with partly aqueous eluents is by no means a new separation mode in LC. The first HPLC applications were published more than 30 years ago, and were for a long time mostly confined to carbohydrate analysis. In the early 1990s new phases started to emerge, and the practice was given a name, hydrophilic interaction chromatography (HILIC). Although the use of this separation mode has been relatively limited, we have seen a sudden increase in popularity over the last few years, promoted by the need to analyze polar compounds in increasingly complex mixtures. Another reason for the increase in popularity is the widespread use of MS coupled to LC. The partly aqueous eluents high in ACN with a limited need of adding salt is almost ideal for ESI. The applications now encompass most categories of polar compounds, charged as well as uncharged, although HILIC is particularly well suited for solutes lacking charge where coulombic interactions cannot be used to mediate retention. The review attempts to summarize the ongoing discussion on the separation mechanism and gives an overview of the stationary phases used and the applications addressed with this separation mode in LC.

A hydrophilic interaction chromatography coupled to a mass spectrometry for the determination of glutathione in plant somatic embryos

An electrospray ionization mass spectrometric (ESI-MS) determination of glutathione (GSH), a sulfur-containing tripeptide (gamma-Glu-Cys-Gly) with regulation and detoxication functions in metabolisms of most living organisms, from nanomolar to micromolar levels is described. A hydrophilic interaction chromatography (HILIC) with an isocratic elution using a mobile phase containing acetonitrile and an aqueous 0.00005% solution of trifluoroacetic acid (60/40%, v/v) was applied for the separation of GSH. The peptide detection was achieved in the presence of L-ascorbic acid which significantly enhanced the signal intensity of the molecular ion GSH [M+H]+ (m/z 308). The calibration curve was linear (R2=0.9995) in the concentration range from 2 nM to 10 microM with a detection limit (LOD, S/N=3) of 0.5 nM. The excellent detection limit, and the excellent selectivity and high reproducibility of this method enabled determination of GSH in a single plant somatic embryo of a Norway spruce (Picea abies). The average amount of GSH in the single somatic embryos (n=18) was 9 pmol per embryo. Owing to our results, it can be supposed that the proposed HILIC/ESI-MS analysis might be used for GSH determination in microscopic cell structures and in single cell analyses.

Peptide separation by Hydrophilic-Interaction Chromatography: a review

Recent developments in the separation of peptides by high-performance liquid chromatography (HPLC) using polar sorbents with less polar eluents are summarized in this review. This separation mode is now commonly referred to as Hydrophilic-Interaction Chromatography (HILIC). The retention mechanism and chromatographic behavior of polar solutes under HILIC conditions are studied on TSKgel Amide-80 columns, which consist of carbamoyl groups bonded to a silica gel matrix, using a mixture of acetonitrile (MeCN)-water containing 0.1% trifluoroacetic acid (TFA). Some applications are given in peptide field using Hydrophilic-Interaction Chromatography.

Analysis of glucosinolates from broccoli and other cruciferous vegetables by hydrophilic interaction liquid chromatography

While methods for the identification and quantification of total plant glucosinolate content typically utilize desulfation of glucosinolates followed by reversed-phase chromatography, the analysis of intact glucosinolates has been problematic. Hydrophilic interaction chromatography offers a novel method for analyzing intact glucosinolates and when performed along with ion-pair reversed-phase chromatography offers a powerful and complementary method for glucosinolate analysis.

Calculation of peptide retention coefficients in normal-phase liquid chromatography

The retention of 121 peptides was studied on a TSK Amide-80 column using solutions containing 0.1% trifluoroacetic acid and an increasing linear gradient of water in acetonitrile. The contribution of each residue to retention was calculated by linear multiple regression analysis. This paper described the contribution values 'hydrophilicity retention coefficients'. The result is an index of hydrophilicity retention coefficients for normal-phase liquid chromatography, analogous to the hydrophobicity indices calculated for the reversed-phase liquid chromatography. The order of residues in the index of one mode was substantially the inverse of the others'. Using the new hydrophilicity retention coefficients, retention times could be predicted for peptides of known amino acid content and sequence.

A tyrosine kinase assay using reverse-phase high-performance liquid chromatography

Reverse-phase HPLC can be used as a very precise and accurate routine assay for peptide phosphorylation by protein kinases that has advantages over other methods. In particular, peptides with native amino acid sequences can be used without the need for radioisotopes. However, reaction conditions that are employed can often present difficulties in recovery and quantitation of phospho- and apo-peptides. Two general problems were encountered; First, variation in the retention times of peptides and an increasing width of the injection front which can interfere with quantitation both resulted from repeated sample injections. These were caused mostly by the presence of carrier bovine serum albumin used to reduce loss of peptides during the reaction and by high concentrations of ATP used to study the kinetics of enzyme catalyzed reactions. These problems were solved by regular washing of the reverse-phase column, thus allowing a broad range of peptide and ATP concentrations to be used. Second, the stability of peptides used in the assay was affected by dithiothreitol in combination with manganese. The former is a common reagent of kinase purifications and the latter is often the metal cofactor used in kinase reactions. Minimizing the concentration of dithiothreitol or using magnesium resolved these difficulties. Consideration of these factors is therefore important when using reverse-phase HPLC to monitor peptide phosphorylation in protein tyrosine kinase assays.

Tyrosine protein kinase assays

Protein kinases form a large family of enzymes that play a major role in a number of live processes. The study of their action is important for the understanding of the transformation mechanisms and of the normal and pathological growth events. The quality of an enzyme assay is often the key point of an enzymatic study. It must be flexible and compatible with various experimental conditions, such as those for the purification process, the screening of inhibitors and the substrate specificity studies. As will be shown in the present review, two categories of substrates, peptidic and proteic, should be distinguished. The use of peptide substrates facilitates the determination of the recognition requirements of the enzyme and of the kinetic effects of even minute variations in their sequence. These linear peptide structures are assumed to mimic a complex interaction between the enzyme and a protein substrate in which distant amino acids in the sequence are vicinal in the folded substrate. Less amenable to a systematic study, but probably more adequate to investigate the natural substrate of a given kinase, are the proteic substrates. Obviously the tools to measure protein kinase activities are not the same in these two cases. The main difficulty in assaying protein kinases is the use of labelled gamma-ATP, mostly at large excess concentration, since the final product of the reaction has to be separated from the non-reacted labelled ATP. In the case of peptide substrates, the difficulty is to separate them from ATP basing on differences of molecular mass. Despite the efforts of many investigators to rely upon differences in solubility, in charges or in "affinity", this separation, which is crucial for the assay, is still an unsolved experimental problem. Chromatographic, as well as electrophoretic assays appeared relatively late in this domain, and more work in assessing new methodologies might bring new breakthroughs in the next few years. Specific, simple and reliable kinase assays are still a major challenge. Their improvement will help to conduct specificity studies, to elucidate complex growth mechanisms in which they are involved and to discover more selective potent inhibitors.

Tyrosine protein kinase inhibition and cancer

The various aspects of the research on tyrosine protein kinase inhibition and its connections with cancer are presented. The emphasis was made on the theoretical low toxic side effects of specific tyrosine protein kinase inhibitors. Particularly, the strategy of finding peptidic substrate-derived inhibitors or modulators is discussed, with an almost complete compendium of the tyrosine protein kinase peptidic substrates published so far. A series of data has been gathered that may serve as a basis for the discovery of selective and specific tyrosine protein kinase inhibitors by screening on molecular and cellular models. The potential of SH2 domain-interfering agents are also presented as a promising route to new anticancer compounds.

High-performance liquid chromatography-based assays of enzyme activities

Interest in using HPLC to assay enzymatic reactions continues to grow as evidenced by the more than 100 papers published during the early 1990s. HPLC can be used for any enzymatic assay that requires separation of substrates and products before quantifying the extent of the reaction. The popularity of HPLC-based assays is due to several reasons: (1) HPLC offers unsurpassed precision, specificity, sensitivity, and reproducibility. (2) Powerful microcomputers and user-friendly software automate the running of samples and collection and processing of data. (3) Current columns, especially C18 packings, separate a very wide variety of samples, and (4) A variety of on-line detectors provide a means to detect virtually any compound. This review surveys recent papers on the development of HPLC-based assays for enzymes that degrade or otherwise modify macromolecules. Methods for assaying enzymes involved in metabolic pathways are also reviewed. Work by the authors in developing HPLC-based assays for mitochondrial enzymes that use GTP/GDP and other nucleotides that cannot be or are not easily assayed by enzyme-coupled assays is discussed. These enzymes include nucleoside diphosphate kinase, succinate thiokinase, and GTP-AMP phosphotransferase. The assays are suitable for determining the submitochondrial compartmentation of enzyme activities. Finally, current and anticipated trends in HPLC technology, including new column packings and the trend toward smaller columns that give faster separations, are reviewed in relation to enzyme assays.

Substrate phosphorylation capacities of the major tyrosine protein kinase from the human promyelocytic cell line, HL-60

The major tyrosine protein kinase, HPK40, isolated from HL-60, the preparation of which is described elsewhere (Ernould, A.P., Ferry, G., Barret, J.M., Genton, A. and Boutin, J.A., Eur. J. Biochem., 214, 503-514), was investigated as to its specificity on a number of peptides and proteins. It was found that HPK40 can phosphorylate histones (except histone H4), casein, acid-treated enolase, actin and tubulin but not calmodulin. Phosphorylation specificity of HPK40 was investigated using over a hundred peptidic structures. HPK40 is not related to the 'src' family and does not phosphorylate efficiently either the tetrapeptide NEYT derived from the pp60src autophosphorylation domain or the corresponding peptide RRsrc, RRLIED-NEYTARG. VALYDYESR from the SH3 domain of pp60c-src is recognized as a substrate with a high phosphorylation level. DEDYIQD, derived from the phosvitin/casein kinase II, was also highly phosphorylated. In order to determine the minimal recognition sequence of HPK40, the phosphorylation of about 60 dito tetrapeptides was investigated. Some of the tetrapeptides, such as *EEYE and NEYE, were well phosphorylated. Even some tripeptides, such as EYE, DYM, TYS and KYE, were recognized by HPK40, while none of the tested dipeptides was recognized as substrate. Sequences of peptides from DRVYHPF (angiotensin), LEEEEEAYGWMDF (minigastrin) and QEEYSAM (from H-ras1) were examined as substrates. The presence of one or several acidic residues on the N alpha-side of tyrosine residue was identified as the only apparently favorable determinant.(ABSTRACT TRUNCATED AT 250 WORDS)

Purification and characterization of the major tyrosine protein kinase from the human promyelocytic cell line, HL60

The major tyrosine protein kinase from HL60 (a human non-differentiated promyelocytic cell line) has been purified almost to homogeneity as judged by silver-stained SDS/PAGE. The procedure involved four chromatographic steps: DEAE-Sepharose, casein-agarose, cibacron-blue--agarose and hexyl-agarose. The purification resulted in more than 1000-fold enrichment in angiotensin II phosphorylation activity. A gel-sizing experiment, labeling with [35S]ATP[gamma s] and autophosphorylation of the enzyme in the presence of [gamma-32P]ATP, all led to the identification of a single protein species with a molecular mass of about 40 kDa. Western blot experiments showed that this protein does not belong to the src family and is not related to the abl and fes oncogene products. Phosphorylation of angiotensin II and casein by this 40-kDa human promyelocytic kinase was stimulated by high ionic strength especially from class IA metal salts. The Km for ATP was 2 microM and the Vmax 3.1 nmol.min-1.mg-1 using angiotensin II as a substrate. The kinase requires the presence of either Mn2+ or Mg2+ for full activity and utilizes ATP or dATP but not GTP as phosphate donor. Based on numerous biochemical observations, it was possible to demonstrate that kinase is different from any other tyrosine protein kinases described in the literature. This 40-kDa protein was used as a molecular tool for testing some tyrosine protein kinase inhibitors described in the literature. It is one of the rare tyrosine protein kinases purified from human cancer cells to date.

Studies of the potency of protein kinase inhibitors on ATPase activities

Tyrosine as well as serine/threonine protein kinase inhibitors have potentially two sites of interaction with their targets: the protein-substrate binding site and the ATP binding site. The latter could be modelized by measuring the capacity of protein kinase inhibitors to inhibit ATPase activities. In order to do so, we assess a novel, highly sensitive HPLC method based on hydrophilic separation of [gamma-32P]ATP and [32P]Pi. The novel assay is presented. Furthermore, the potency of 13 protein kinase inhibitors was tested on two types of ATPase, namely: apyrase and partially purified liver mitochondria F1-ATPase. The method described for the assay of ATPase can be used with almost any type of enzyme catalyzing this activity. Only cibacron blue and suramin show interesting capacities in inhibiting these ATPase activities pointing out that several widely used protein kinase inhibitors are at least somewhat specific in that they do not inhibit these two ATPases.