pH/Organic Solvent Double-Gradient Reversed-Phase HPLC

QSRR Modeling for Metabolite Standards Analyzed by Two Different Chromatographic Columns Using Multiple Linear Regression

Modified quantitative structure retention relationships (QSRRs) are proposed and applied to describe two retention data sets: A set of 94 metabolites studied by a hydrophilic interaction chromatography system under organic content gradient conditions and a set of tryptophan and its major metabolites analyzed by a reversed-phase chromatographic system under isocratic as well as pH and/or simultaneous pH and organic content gradient conditions. According to the proposed modification, an additional descriptor is added to a conventional QSRR expression, which is the analyte retention time, tR(R), measured under the same elution conditions, but in a second chromatographic column considered as a reference one. The 94 metabolites were studied on an Amide column using a Bare Silica column as a reference. For the second dataset, a Kinetex EVO C18 and a Gemini-NX column were used, where each of them was served as a reference column of the other. We found in all cases a significant improvement of the performance of the QSRR models when the descriptor tR(R) was considered.

High-throughput absolute quantification of proteins using an improved two-dimensional reversed-phase separation and quantification concatemer (QconCAT) approach

Stable isotope dilution-selective reaction monitoring-mass spectrometry (SID-SRM-MS) has been widely used for the absolute quantitative analysis of proteins. However, when performing the large-scale absolute quantification of proteins from a more complex tissue sample, such as mouse liver, in addition to a high-throughput approach for the preparation and calibration of large amounts of stable-isotope-labelled internal standards, a more powerful separation method prior to SRM analysis is also urgently needed. To address these challenges, a high-throughput absolute quantification strategy based on an improved two-dimensional reversed-phase (2D RP) separation and quantification concatemer (QconCAT) approach is presented in this study. This strategy can be used to perform the simultaneous quantification of hundreds of proteins from mouse liver within one week of total MS measurement time. By using calibrated synthesised peptides from the protein glutathione S-transferase (GST), large amounts of GST-tagged QconCAT internal standards corresponding to hundreds of proteins can be accurately and rapidly quantified. Additionally, using an improved 2D RP separation method, a mixture containing a digested sample and QconCAT standards can be efficiently separated and absolutely quantified. When a maximum gradient of 72 min is employed in the first LC dimension, resulting in 72 fractions, identification and absolute quantification experiments for all fractions can be completed within one week of total MS measurement time. The quantification approach developed here can further extend the dynamic range and increase the analytical sensitivity of SRM analysis of complex tissue samples, thereby helping to increase the coverage of absolute quantification in a whole proteome.

A fast workflow for identification and quantification of proteomes

The current in-depth proteomics makes use of long chromatography gradient to get access to more peptides for protein identification, resulting in covering of as many as 8000 mammalian gene products in 3 days of mass spectrometer running time. Here we report a fast sequencing (Fast-seq) workflow of the use of dual reverse phase high performance liquid chromatography - mass spectrometry (HPLC-MS) with a short gradient to achieve the same proteome coverage in 0.5 day. We adapted this workflow to a quantitative version (Fast quantification, Fast-quan) that was compatible to large-scale protein quantification. We subjected two identical samples to the Fast-quan workflow, which allowed us to systematically evaluate different parameters that impact the sensitivity and accuracy of the workflow. Using the statistics of significant test, we unraveled the existence of substantial falsely quantified differential proteins and estimated correlation of false quantification rate and parameters that are applied in label-free quantification. We optimized the setting of parameters that may substantially minimize the rate of falsely quantified differential proteins, and further applied them on a real biological process. With improved efficiency and throughput, we expect that the Fast-seq/Fast-quan workflow, allowing pair wise comparison of two proteomes in 1 day may make MS available to the masses and impact biomedical research in a positive way.

[Reversed-phase liquid chromatography with double gradient elution for the separation and mass spectrometric analysis of peptides]

Highly effective separation of complex peptide mixture is a prerequisite for protein identification with high coverage in proteomics. Currently, peptide mixture is separated by two-dimensional liquid chromatography (2D-LC), ion exchange chromatography as the first dimension and reversed-phase chromatography as the second dimension, in Shotgun proteomics. Though the 2D-LC is now widely used, its separation efficiency still needs further improvement. In this work, the first dimensional separation was performed by the pH and organic solvent double-gradient elution. And then the two fractions, one from the early eluted section and the other from the later eluted section (with equal time intervals) were pooled and analyzed by MS/MS. The experimental results from the protein mixture of saccharomyces cerevisiae lysate showed that the separation by pH and organic solvent double-gradient elution, RP-HPLC-nanoRPLC coupled with MS/MS identified 567 more yeast protein groups (3 035 peptides) over strong cation exchange chromatography-nanoRPLC coupled with MS/MS. The pI values and relative molecular masses of identified peptides ranged from 3.42 to 12.01, and from 587.67 to 3 499.79, respectively. The pI values and relative molecular masses of identified proteins ranged from 3.82 to 12.19 and from 3 446.55 to 432 905, respectively. These results indicated that this new 2DLC-MS method has the advantages over the conventional Shotgun method, and were expected to be applied in the separation of complex samples for proteomic studies in the future.

Simultaneous determination of pKa and lipophilicity by gradient RP HPLC

High-performance methods of testing of drug candidates for properties of pharmacokinetics and pharmacodynamics importance, in particular lipophilicity and acidity, are necessary to overcome innovation stagnation in the pharmaceutical industry. Reversed-phase high-performance liquid chromatography (RP HPLC) might be a unique tool for the determination of both pKa and the apparent (pH-dependent) partition coefficient, applicable in high-throughput analysis of multicomponent mixtures, e.g., samples originating from automated synthesis. In this work, the pH/organic modifier gradient RP HPLC is presented as a means of simultaneous determination of an analyte's acidity and lipophilicity. The approach consists of retention measurements in a series of methanol gradient runs differing in pH range and duration of the gradient. Two different models of the influence of pH on retention in organic modifier gradient RP HPLC are compared regarding the quality of the simultaneously determined lipophilicity and dissociation constants. Advantages of the proposed approach over currently employed procedures are that it can be applied to compound mixtures, it requires only minute amounts of substances, and pKa values can be determined in the range 3-10 units and lipophilicity in the range 0-7 units. Verification of the reliability of the parameters determined by the new method was demonstrated on a series of 93 acidic and basic drug analytes.

Theory of Stepwise Gradient Elution in Reversed-Phase Liquid Chromatography Coupled with Flow Rate Variations: Application to Retention Prediction and Separation Optimization of a Set of Amino Acids

The coupling of stepwise mobile phase gradient elution and flow programming is proposed as an integrated approach to the general elution problem in reversed-phase liquid chromatography. A model is developed to describe the above separation process performed under simultaneous programming of two separation parameters by extending our previous work on the rigorous derivation of the fundamental equation governing the concentration gradient of organic modifier in the mobile phase, that is, a single gradient elution mode (Anal. Chem. 2005, 77, 5670-5677). The theory was tested in the retention prediction and separation optimization of 18 o-phthalaldehyde derivatives of amino acids in eluting systems modified by acetonitrile or methanol. The retention prediction obtained for all solutes under all dual-mode gradient conditions was excellent. In addition, it has been shown that the combination of mobile phase and flow rate programming modes is particularly favorable, whereas the separations among the analytes were considerably improved by using the acetonitrile eluting system, as compared to those obtained by the methanol system.

Comprehensive multi-dimensional liquid chromatographic separation in biomedical and pharmaceutical analysis: a review

'Multi-dimensional' liquid separations have a history almost as long as chromatography. In multi-dimensional chromatography the sample is subjected to more than one separation mechanism; each mechanism is considered an independent separation dimension. The separations can be carried out either offline via fraction collection, or directly coupled online. Early multi-dimensional separations using combinations of paper chromatography, electrophoresis and gels, in both planar and columnar modes are reviewed. Developments in HPLC have increased the number of measurable analytes in ever more complex matrices, and this has led to the concept of 'global metabolite profiling'. This review focuses on the theory and practice of modern 'comprehensive' multi-dimensional liquid chromatography when applied to biomedical and pharmaceutical analysis.

Liquid chromatography-mass spectrometry and related techniques for purity assessment in early drug discovery

The combination of HPLC and MS has become the most valuable analytical tool to determine the identity and purity of a drug substance in the drug discovery arena over the past decade. This article describes different LC/MS configurations and their broad applicability to meet the fundamental analytical requirements involved in discovering new drugs. In addition, the value of chemiluminescence nitrogen detection for absolute purity determination and the convenience of CE as an orthogonal separation technique to HPLC are also discussed. In summary, LC/MS-based methodologies that implicate automation, various levels of throughput and open access systems have proved to be an integral part of the drug discovery process. As a result, the paradigm of high-quality/-quantity information is fulfilled in a timely fashion.

Theoretical opportunities and actual limitations of pH gradient HPLC

In a series of reports published recently by our laboratory comprehensive theory and experimental conditions were established for reversed-phase high-performance liquid chromatography (RP HPLC) employing the programmed pH gradient of mobile phase. A procedure was developed providing, rapidly and conveniently, the acidity (pK(a)) of weak acids and bases and their lipophilicity (hydrophobicity) log k(w). The basis of the double-gradient RP HPLC, employing simultaneous gradients of organic modifier content and mobile phase pH, was also elaborated. The fundamentals of the approach are presented briefly and systematically and its advantages and limitations are discussed. It is demonstrated that the newly introduced pH gradient method increases the analytical versatility of RP HPLC and our understanding of its physicochemical basis.