Comparison of Targeted Mass Spectrometry Techniques with an Immunoassay: A Case Study for HSP90α.

PURPOSE: The objective of this study is to better understand factors governing the variability and sensitivity in SRM and PRM, compared to immunoassay. EXPERIMENTAL DESIGN: A 2D-LC-MS/MS-based SRM and PRM assay is developed for quantitative measurements of HSP90α in serum. Forty-three control sera are compared by SRM, PRM, and ELISA following the manufacturer's instructions. Serum samples are trypsin-digested and fractionated by strong cation exchange chromatography prior to SRM and PRM measurements. Analytical parameters such as linearity, LOD, LOQ, repeatability, and reproducibility of the SRM, PRM, and ELISA are determined. RESULTS: PRM data obtained by high-resolution MS correlate better with ELISA measurements than SRM data measured on a triple quadrupole mass spectrometer. While all three methods (SRM, PRM, and ELISA) are able to quantify HSP90α in serum at the ng mL-1 level, the use of PRM on a high-resolution mass spectrometer reduces variation and shows comparable sensitivity to immunoassay. CONCLUSIONS AND CLINICAL RELEVANCE: Using fractionation, it is possible to measure ng mL-1 levels of HSP90α in a reproducible, selective, and sensitive way using PRM in serum. This opens up the possibility to use PRM in a multiplexed way as an attractive alternative for immunoassays without the use of antibodies or comparable binders.

A 6-alkylsalicylate histone acetyltransferase inhibitor inhibits histone acetylation and pro-inflammatory gene expression in murine precision-cut lung slices.

Lysine acetylations are post-translational modifications of cellular proteins, that are crucial in the regulation of many cellular processes. Lysine acetylations on histone proteins are part of the epigenetic code regulating gene expression and are installed by histone acetyltransferases. Observations that inflammatory lung diseases, such as asthma and chronic obstructive pulmonary disease, are characterized by increased histone acetyltransferase activity indicate that development of small molecule inhibitors for these enzymes might be a valuable approach towards new therapies for these diseases. The 6-alkylsalicylate MG149 is a candidate to explore this hypothesis because it has been demonstrated to inhibit the MYST type histone acetyltransferases. In this study, we determined the Ki value for inhibition of the MYST type histone acetyltransferase KAT8 by MG149 to be 39 ± 7.7 µM. Upon investigating whether the inhibition of histone acetyltransferases by MG149 correlates with inhibition of histone acetylation in murine precision-cut lung slices, inhibition of acetylation was observed using an LC-MS/MS based assay on histone H4 res 4-17, which contains the target lysine of KAT8. Following up on this, upon treatment with MG149, reduced pro-inflammatory gene expression was observed in lipopolysaccharide and interferon gamma stimulated murine precision-cut lung slices. Based on this, we propose that 6-alkylsalicylates such as MG149 have potential for development towards applications in the treatment of inflammatory lung diseases.

Site-specific quantification of lysine acetylation in the N-terminal tail of histone H4 using a double-labelling, targeted UHPLC MS/MS approach.

We developed a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the site-specific quantification of lysine acetylation in the N-terminal region of histone H4 by combining chemical derivatization at the protein and peptide levels with digestion using chymotrypsin and trypsin. Unmodified ε-amino groups were first modified with propionic acid anhydride and the derivatized protein digested with trypsin and chymotrypsin. The newly formed peptide N-termini were subjected to a second derivatization step with d6- (heavy) or d0- (light) acetic acid anhydride. Samples were mixed at different ratios and peptides monitored by multiple reaction monitoring (MRM) LC-MS/MS. The method was validated in terms of linearity (R(2) ≥ 0.94), precision (RSD ≤ 10%), and accuracy (≤27%) and used to assess the effect of the histone deacetylase (HDAC) inhibitors SAHA and MS-275 in the murine macrophage-like cell line RAW 264.7. SAHA and MS-275 showed site-specific effects on the acetylation levels of K5 and K8 with the K5(Ac)-K8 and K5-K8(Ac) peptides increasing 2.5-fold and 5-fold upon treatment with SAHA and MS-275, respectively. Assessing lysine acetylation in a site-specific manner is important for gaining a better understanding of the effects of HDAC inhibitors and for clarifying disease mechanisms where lysine acetylation plays a role.

The histone acetyltransferase p300 inhibitor C646 reduces pro-inflammatory gene expression and inhibits histone deacetylases.

Lysine acetylations are reversible posttranslational modifications of histone and non-histone proteins that play important regulatory roles in signal transduction cascades and gene expression. Lysine acetylations are regulated by histone acetyltransferases as writers and histone deacetylases as erasers. Because of their role in signal transduction cascades, these enzymes are important players in inflammation. Therefore, histone acetyltransferase inhibitors could reduce inflammatory responses. Among the few histone acetyltransferase inhibitors described, C646 is one of the most potent (Ki of 0.4µM for histone acetyltransferase p300). C646 was described to affect the NF-κB pathway; an important pathway in inflammatory responses, which is regulated by acetylation. This pathway has been implicated in asthma and COPD. Therefore, we hypothesized that via regulation of the NF-κB signaling pathway, C646 can inhibit pro-inflammatory gene expression, and have potential for the treatment of inflammatory lung diseases. In line with this, we demonstrate here that C646 reduces pro-inflammatory gene expression in RAW264.7 murine macrophages and murine precision-cut lung slices. To unravel its effects on cellular substrates we applied mass spectrometry and found, counterintuitively, a slight increase in acetylation of histone H3. Based on this finding, and structural features of C646, we presumed inhibitory activity of C646 on histone deacetylases, and indeed found inhibition of histone deacetylases from 7µM and higher concentrations. This indicates that C646 has potential for further development towards applications in the treatment of inflammation, however, its newly discovered lack of selectivity at higher concentrations needs to be taken into account.

A panel of regulated proteins in serum from patients with cervical intraepithelial neoplasia and cervical cancer.

We developed a discovery-validation mass-spectrometry-based pipeline to identify a set of proteins that are regulated in serum of patients with cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancer using iTRAQ, label-free shotgun, and targeted mass-spectrometric quantification. In the discovery stage we used a "pooling" strategy for the comparative analysis of immunodepleted serum and revealed 15 up- and 26 down-regulated proteins in patients with early- (CES) and late-stage (CLS) cervical cancer. The analysis of nondepleted serum samples from patients with CIN, CES, an CLS and healthy controls showed significant changes in abundance of alpha-1-acid glycoprotein 1, alpha-1-antitrypsin, serotransferrin, haptoglobin, alpha-2-HS-glycoprotein, and vitamin D-binding protein. We validated our findings using a fast UHPLC/MRM method in an independent set of serum samples from patients with cervical cancer or CIN and healthy controls as well as serum samples from patients with ovarian cancer (more than 400 samples in total). The panel of six proteins showed 67% sensitivity and 88% specificity for discrimination of patients with CIN from healthy controls, a stage of the disease where current protein-based biomarkers, for example, squamous cell carcinoma antigen (SCCA), fail to show any discrimination. Additionally, combining the six-protein panel with SCCA improves the discrimination of patients with CES and CLS from healthy controls.

Multidimensional separation of tryptic peptides from human serum proteins using reversed-phase, strong cation exchange, weak anion exchange, and fused-core fluorinated stationary phases.

Proteome profiling of crude serum is a challenging task due to the wide dynamic range of protein concentrations and the presence of high-abundance proteins, which cover >90% of the total protein mass in serum. Peptide fractionation on strong cation exchange, weak anion exchange in the electrostatic repulsion hydrophilic interaction chromatography (ERLIC) mode, RP C18 at pH 2.5 (low pH), fused-core fluorinated at pH 2.5, and RP C18 at pH 9.7 (high pH) stationary phases resulted in two to three times more identified proteins and three to four times more identified peptides in comparison with 1D nanoChip-LC-MS/MS quadrupole TOF analysis (45 proteins, 185 peptides). The largest number of peptides and proteins was identified after prefractionation in the ERLIC mode due to the more uniform distribution of peptides among the collected fractions and on the RP column at high pH due to the high efficiency of RP separations and the complementary selectivity of both techniques to low-pH RP chromatography. A 3D separation scheme combining ERLIC, high-pH RP, and low-pH nanoChip-LC-MS/MS for crude serum proteome profiling resulted in the identification of 208 proteins and 1088 peptides with the lowest reported concentration of 11 ng/mL for heat shock protein 74.

Simultaneous serum desalting and total protein determination by macroporous reversed-phase chromatography.

Macroporous reversed-phase (mRP) chromatography was successfully used to develop an accurate and precise method for total protein in serum. The limits of detection (0.83 µg, LOD) and quantification (2.51 µg, LOQ) for the mRP method are comparable with those of the widely used micro BCA protein assay. The mRP method can be used to determine the total protein concentration across a wide dynamic range by detecting chromatographic peaks at 215 nm and 280 nm. The method has the added advantage of desalting and denaturing proteins, leading to more complete digestion by trypsin and to better LC-MS-MS identification in shotgun proteomics experiments.

Glycopeptide enrichment and separation for protein glycosylation analysis.

Protein glycosylation plays key roles in many biological processes. In addition, alterations in protein glycosylation have been related to different diseases, as well as may affect the properties of recombinant proteins used as human therapeutics. For this reason, protein glycosylation analysis is of main interest in biomedical and biopharmaceutical research. Although recent advances in LC-MS analysis have made possible glycoprotein glycosylation site identification, characterization of glycoprotein glycan structures, as well as glycoprotein identification and quantification, protein glycosylation analysis in complex samples still remains a difficult task. This is due to low proportions of glycopeptides in comparison to peptides obtained after glycoprotein digestion, the suppression of the glycopeptide MS signals in the presence of peptides, and the high heterogeneity of glycopeptides. Thus, in the recent years, continuous efforts have been devoted to the development of glycopeptide enrichment and separation strategies to facilitate and improve glycoprotein glycosylation analysis in complex samples. This review summarizes the different methodologies that can be employed for glycopeptide enrichment/separation from complex samples including methods based on lectin affinity enrichment, covalent interactions, or chromatographic separations and solid-phase extraction.

Thin-layer chromatographic plates with monolithic layer of silica: production, physical-chemical characteristics, separation capabilities.

The technique for production of thin-layer chromatographic plates with fixed monolithic layer of sorbent was developed on the basis of investigation of factors affecting sorption capacity, sorption kinetics and mechanical stability of monoliths. The optimal reaction mixture for sol-gel synthesis of monoliths consisted of tetraethoxysilane, buffer solution with pH 7.4, N,N-dimethylformamide, ethanol, polyethyleneglycol with molecular weight 1000 and cetylpyridinium chloride in molar ratio 1.0:4.6:1.4:7.6:0.26:8×10(-3). On the basis of analysis of sorption kinetics of malachite green on the monoliths it was concluded that mechanism of sorption includes chemisorption. The optimized conditions for fixing the monolithic layer on the carrier and its drying allow obtaining undisturbed monolithic layer, which was used for test mixtures separation. The increase of monolithic layer thickness in comparison with ultrathin-layer chromatographic plates allows detecting visually at reasonable concentrations and loaded sample volumes the spots of food and synthetic dyes.

Classification of gasoline by octane number and light gas condensate fractions by origin with using dielectric or gas-chromatographic data and chemometrics tools.

The approach for classification of gasoline by octane number and light gas condensate fractions by origin with using dielectric permeability data has been proposed and compared with classification of same samples on the basis of gas-chromatographic data. The precision of dielectric permeability measurements was investigated by using ANOVA. The relative standard deviation of dielectric permeability was in the range from 0.3 to 0.5% for the range of dielectric permeability from 1.8 to 4.4. The application of exploratory chemometrics tools (cluster analysis and principal component analysis) allow to explicitly differentiate the gasoline and light gas condensate fractions into groups of samples related to specific octane number or origin. The neural networks allow to perfectly classifying the gasoline and light gas condensate fractions.

Aliphatic carboxylic acids and alcohols as efficiency and elution strength enhancers in micellar liquid chromatography.

Micellar liquid chromatography (MLC) uses surfactant solutions as mobile phases with added organic additives to enhance both the elution strength and the chromatographic efficiency. Two aliphatic carboxylic acids (1-butanoic and 1-pentanoic) were used as MLC additives and compared with the two corresponding alcohols (1-butanol, 1-pentanol) in terms of elution strength, efficiency and selectivity. A set of 11 phenol derivatives was used as probe compounds. All micellar mobile phases were prepared with sodium dodecylsulfate (SDS) with concentration ranging from 0.05 to 0.15M and the modifier content within 1.0 and 5.0% (v/v). The elution strength of different mobile phases containing a constant amount of SDS and different amounts of modifiers; and mobile phases containing a constant amount of modifier and different SDS concentration were determined and discussed. The effect of the acid modifiers on efficiency was studied constructing van Deemter plots that showed no minimum within the 0.01-0.7mL/min flow rate range studied. Temperature effects were also studied constructing the classical van't Hoff plots. The slight curvature of the plots in the 25-70 degrees C range may indicate some modification of the surfactant-bonded moiety layer on the stationary phase surface. Since no definitive advantage of the use of aliphatic acids were established compared to their alcohol counterpart, their terrible smell will probably preclude their use as MLC organic modifiers.

Aliphatic carboxylic acids as new modifiers for separation of 2,4-dinitrophenyl amino acids by micellar liquid chromatography.

The possibilities of isocratic separation of 2,4-dinitrophenyl derivatives of 12 amino acids that considerably differ in hydrophobicity by micellar mobile phases with different organic modifiers have been discussed. For the first time aliphatic carboxylic acids have been used as modifiers of micellar eluent in micellar liquid chromatography with C18 columns. Elution strength of hybrid micellar phases on the basis of sodium dodecylsulfate and aliphatic carboxylic acids increases in sequence: acetic

Micellar liquid chromatography retention model based on mass-action concept of micelle formation.

Mass-action model of surfactant micelle formation has been used to develop a conceptual retention model in micellar liquid chromatography (MLC). The retention model bases on the consideration of the changes of the sorbate microenvironment at its transferring from the mobile phase (hybrid micellar eluent) to the stationary phase (a modified surface of alkyl-bounded sorbent). Principal retention equation contains the characteristics of hybrid micelles (critical micelle concentration, degree of counterion binding, partition coefficient of modifier between aqueous solution and micellar pseudo-phase) as well as three fitting parameters. The fitting parameters are an absolute term and coefficients that are equal to the number of molecules of surfactant and modifier, which are attached/detached by sorbate transferring from a hybrid micellar eluent to a modified surface of the stationary phase. On the MLC separation of five antibiotics of rubomicin derivatives and four esters of 4-hydroxybenzoic acid the model of the change of sorbate microenvironment has been tested. The adequateness of model to experimental data has been shown. A simple three-parameter function connecting log k with log cS and log cR that provides a high goodness-of-fit follows from principal retention equation (cS and cR are the molar concentrations of surfactant and organic modifier in the micellar eluent, respectively).

Heteroscedasticity of retention factor and adequate modeling in micellar liquid chromatography.

The two concepts of micelle formation (pseudo-phase and mass-action) could be the basis of retention models in micellar liquid chromatography (MLC). The separation of 4-hydroxybenzoic acid esters and seven polyaromatic hydrocarbons were performed to study the repeatability of retention factor in MLC. The full two factor experimental design was used for studying the dependence of retention factor variance on mobile phase composition (sodium dodecylsulfate, 1-butanol). The experimentally observed heteroscedasticity and perturbations after linearization were taken into account by using statistical weights obtained on the basis of errors propagation law and the modeling of retention by non-weighted and weighted least squares method was performed. The mechanistical retention models based on pseudo-phase and mass-action concepts of micelle formation were compared by fitting quality and prediction capability and high robustness of bilogarithmic dependence was observed. The significance of retention factor heteroscedasticity for retention hydrophobicity relationships was shown.