Principles and applications of Multidimensional Protein Identification Technology

Multidimensional chromatography coupled to tandem mass spectrometry is an emerging technique for the analysis of proteomes and is rapidly being implemented by many researchers for proteomic analysis. In this technology profile, a particular proteomic approach known as multidimensional protein identification technology (MudPIT) is discussed. In MudPIT, a biphasic microcapillary column is packed with high-performance liquid chromatography grade reversed phase and strong cation exchange packing materials, loaded with a complex peptide mixture and placed in line with quaternary high-performance liquid chromatography and a tandem mass spectrometer. MudPIT has the capability to analyze highly complex proteomic mixtures such as whole proteomes, organelles and protein complexes.     

Affinity-purification coupled to mass spectrometry: basic principles and strategies

Identifying the interactions established by a protein of interest can be a critical step in understanding its function. This is especially true when an unknown protein of interest is demonstrated to physically interact with proteins of known function. While many techniques have been developed to characterize protein-protein interactions, one strategy that has gained considerable momentum over the past decade for identification and quantification of protein-protein interactions, is affinity-purification followed by mass spectrometry (AP-MS). Here, we briefly review the basic principles used in affinity-purification coupled to mass spectrometry, with an emphasis on tools (both biochemical and computational), which enable the discovery and reporting of high quality protein-protein interactions.     

Immunoaffinity techniques coupled to mass spectrometry for the analysis of human peptide hormones: advances and applications

Introduction: The accurate and comprehensive determination of peptide hormones from biological fluids has represented a considerable challenge to analytical chemists for decades. Besides long-established bioanalytical ligand binding assays (or ELISA, RIA, etc.), more and more mass spectrometry-based methods have been developed recently for purposes commonly referred to as targeted proteomics. Eventually the combination of both, analyte extraction by immunoaffinity and subsequent detection by mass spectrometry, has shown to synergistically enhance the test methods’ performance characteristics.

Areas covered: The review provides an overview about the actual state of existing methods and applications concerning the analysis of endogenous peptide hormones. Here, special focus is on recent developments considering the extraction procedures with immobilized antibodies, the subsequent separation of target analytes, and their detection by mass spectrometry.

Expert commentary: Key aspects of procedures aiming at the detection and/or quantification of peptidic analytes in biological matrices have experienced considerable improvements in the last decade, particularly in terms of the assays’ sensitivity, the option of multiplexing target compounds, automatization, and high throughput operation. Despite these advances and progress as expected to be seen in the near future, immunoaffinity purification coupled to mass spectrometry is not yet a standard procedure in routine analysis compared to ELISA/RIA.     

Improved high-performance liquid chromatographic method in the analysis of adenovirus particles

We developed a HPLC method on a novel continuous bed matrix (UNO Q, Bio-Rad) for the direct quantification of adenoviral type 5 (Ad5) particles produced in 293S Human Embryonic Kidney cells and compared this with an existing HPLC method on a conventional ion-exchange resin (Resource Q, Pharmacia). The 293S cell extract contained large amounts of DNA. This contaminated the viral peak on the Resource Q column and only after Benzonase treatment was it possible to quantify the viral particles in the cell extract. In contrast, the virus peak on the UNO Q column was resolved from the DNA which eliminates the need for pretreatment of the sample with Benzonase. Cross-analysis of the Ad5 fraction from the UNO Q column using a size-exclusion HPLC column revealed no additional contaminating peaks. We conclude that the purity of the Ad5 virus peak on the continuous bed matrix UNO Q column was superior to the purity of the virus on the conventional Resource Q column, which is essential for reliable quantification.     

Comparison of originator and biosimilar therapeutic monoclonal antibodies using comprehensive two-dimensional liquid chromatography coupled with time-of-flight mass spectrometry

As research, development, and manufacturing of biosimilar protein therapeutics proliferates, there is great interest in the continued development of a portfolio of complementary analytical methods that can be used to efficiently and effectively characterize biosimilar candidate materials relative to the respective reference (i.e., originator) molecule. Liquid phase separation techniques such as liquid chromatography and capillary electrophoresis are powerful tools that can provide both qualitative and quantitative information about similarities and differences between reference and biosimilar materials, especially when coupled with mass spectrometry. However, the inherent complexity of these protein materials challenges even the most modern one-dimensional (1D) separation methods. Two-dimensional (2D) separations present a number of potential advantages over 1D methods, including increased peak capacity, 2D peak patterns that can facilitate unknown identification, and improvement in the compatibility of some separation methods with mass spectrometry. In this study, we demonstrate the use of comprehensive 2D-LC separations involving cation-exchange (CEX) and reversed-phase (RP) separations in the first and second dimensions to compare 3 reference/biosimilar pairs of monoclonal antibodies (cetuximab, trastuzumab and infliximab) that cover a range of similarity/disimilarity in a middle-up approach. The second dimension RP separations are coupled to time-of-flight mass spectrometry, which enables direct identification of features in the chromatograms obtained from mAbs digested with the IdeS enzyme, or digestion with IdeS followed by reduction with dithiothreitol. As many as 23 chemically unique mAb fragments were detected in a single sample. Our results demonstrate that these rich datasets enable facile assesment of the degree of similarity between reference and biosimilar materials.     

Chiral separation principles in chromatographic and electromigration techniques

Almost half of the drugs in use today are chiral. It is well established that the pharmacological activity is mostly restricted to one of the enantiomers (eutomer). There can be qualitative and quantitative differences in the activity of the enantiomers. In many cases, the inactive enantiomer (distomer) shows unwanted side effects or even toxic effects. Even if the side effects are not that drastic, the distomer has to be metabolized and this represents an unnecessary burden for the organism. Therefore, the development of methods for the separation of enantiomers, both on analytical and preparative scale, has become increasingly important. Chromatographic techniques such as thin layer chromatography (TLC), gas chromatography (GC), supercritical fluid chromatography (SFC), and above all high-performance liquid chromatography (HPLC) have been used for enantiomer separation for about two decades. More recently, electromigration techniques, such as capillary electrophoresis and capillary electrochromatography, have been shown to be powerful alternatives to chromatographic methods. This review gives a short overview of different chiral separation principles and their application. Several new developments are discussed.     

Micellar liquid chromatographic determination of metformin hydrochloride using fluorimetric detection after pre‐column derivatization: application to pharmacokinetic parameters in immediate and sustained release formulations

An accurate and selective method using micellar liquid chromatography was developed to determine metformin hydrochloride both in its pharmaceutical dosage forms and human plasma. Separation was conducted using a Zorbax SB‐Phenyl (250 × 4.6 mm id) stainless steel column at ambient temperature after pre‐column derivatization with 9,10‐phenanthraquinone. A mobile phase composed of 0.1 M sodium dodecyl sulfate, 10% 1‐propanol and triethylamine (0.3%) in 0.02 M phosphoric acid, adjusted to pH 2.5, was used at a flow rate of 1 ml/min with fluorimetric detection at 450 nm after excitation at 306 nm. The proposed method showed high sensitivity with limit of quantification of 0.35 μg/ml and limit of detection of 0.23 μg/ml, being linear from 0.5 to 3.0 μg/ml. Being highly sensitive, the method could be applied to spiked human plasma, and also to follow the pharmacokinetic parameters of the studied drug in healthy volunteers after administration of both its immediate and sustained release tablet formulations. Such procedures were carried out without any extraction steps, which improves the accuracy and precision of the proposed method when applied to human plasma. Detailed validation procedures were also carried out giving results in accordance with the comparison method. The proposed method has also the advantage of being environmentally safe, where the use of organic solvents is highly limited in comparison with other traditional chromatographic separation methods that depend mainly on a high proportion of organic modifiers. This concept, in turn, emphasizes the application of green chemistry in the analysis of pharmaceutical products. The simplicity, relatively low cost and short analysis time of the suggested method makes it a candidate for routine quality control work.     

5-Methyltetrahydrofolic acid and folic acid measured in plasma with liquid chromatography tandem mass spectrometry: applications to folate absorption and metabolism

We describe a liquid chromatography (LC) tandem mass spectrometry (MS-MS) method for the determination of 5-methyltetrahydrofolic acid (5-methylTHF) and folic acid concentrations and enrichments in human plasma. It was used to study absorption and initial metabolism in five volunteers with two simultaneously administered oral test doses ([(13)C(6)]folic acid in capsules and [(2)H(2)]folic acid in a drink). [(13)C(5)]5-methylTHF and [(2)H(4)]folic acid were used as internal standards. Plasma samples (2 ml) were purified using folate binding protein affinity columns, followed by a concentration step. After LC separation, folates were detected using positive electrospray ionization MS-MS under multiple reaction monitoring conditions. Calibrations were linear for 5-methylTHF over the range 1.2 x 10(-11) (=limit of detection) to 3.2 x 10(-7)mol/L and for folic acid over the range 5 x 10(-10) (=limit of detection) to 4.5 x 10(-8)mol/L. For 5-methylTHF concentration in plasma, intraassay coefficient of variation was within 8.6% (and for unlabeled 5-methylTHF it was within 2.8%) and interassay coefficient of variation was within 9.0%. For folic acid concentrations these coefficient of variations were within 7.5% and within 6.5%, respectively. The [(13)C(6)] and [(2)H(2)] isotopomers of folic acid and 5-methylTHF were measured in the plasma of each volunteer for 8h. After accounting for the time delay due to capsule opening, the modeling results showed no significant differences in absorption time, first pass effect, and elimination rate in the folic acid test doses in capsule or drink. We conclude that LC-MS-MS offers increased sensitivity for quantification of plasma concentrations and enrichments of 5-methylTHF and folic acid and is applicable to stable-isotope studies in humans.     

Development of multidimensional liquid chromatography and application in proteomic analysis

As a complementary approach to 2D-PAGE, multidimensional liquid chromatography (MDLC) separation methods have been widely applied in all kinds of biological sample investigations. MDLC coupled with mass spectrometry is playing an important role in proteome research owing to its high speed, high resolution and high sensitivity. Among MDLC strategies, ion-exchange chromatography together with reversed-phase LC is still a most widely used chromatography in proteome analysis; other chromatographic methods are also frequently used in protein prefractionations. Recent MDLC technologies and applications to a variety of proteome analyses have achieved great development. The diversity of combinations of different chromatography modes to set up MDLC systems was demonstrated and discussed. Novel developments of MDLC techniques such as ultra-pressure system, array-based separation and monolithic material are also included in this article.     

高效液相尺寸排阻色谱-多角度激光散射定量检测灭活禽流感病毒抗原中完整病毒颗粒

本研究旨在建立一种灭活禽流感病毒原料液中完整病毒颗粒准确定量的方法。针对直接采用高效液相尺寸排阻色谱法（high performance size exclusion chromatography,HPSEC）检测灭活禽流感病毒原液存在杂质干扰的问题,首先以H5N8型抗原为对象,分别考察了聚乙二醇（polyethylene glycol,PEG）沉淀和离子交换色谱法（ion exchange chromatography,IEC）进行预处理。在优化条件下,经DEAE FF阴离子交换层析纯化预处理,杂蛋白去除率为86.87%,病毒血凝回收率为100%。HPSEC分析预处理后的样品,8.5–10.0 min处色谱峰样品电泳检测显示主要为H5N8病毒蛋白,动态光散射分析平均粒径为127.7 nm,推测为完整病毒特征峰;在IEC预处理后的样品中加入抗体进行HPSEC检测,8.5-10.0 min处特征峰消失,显示IEC预处理有效去除了杂质干扰。通过将HPSEC与多角度激光散射技术（multi-angle laser scattering technique,MALLS）联用,可以准确获得样品中完整病毒颗粒的数量,且病毒颗粒数与色谱峰面积具有良好线性关系（R²=0.997）。建立的IEC预处理-HPSEC-MALLS检测方法应用于其他亚型（H7N9）、批次和浓度的病毒原液中完整病毒颗粒数的准确检测,均具有良好适用性,且重复性好,相对标准偏差（relative standard deviation,RSD）<5%,n=3。     

Near infrared spectroscopy compared to liquid chromatography coupled to mass spectrometry and capillary electrophoresis as a detection tool for peptide reaction monitoring

Peptide interaction is normally monitored by liquid chromatography (LC), liquid chromatography coupled to mass spectrometry (LC-MS), mass spectrometric (MS) methods such as MALDI-TOF/MS or capillary electrophoresis (CE). These analytical techniques need to apply either high pressure or high voltages, which can cause cleavage of newly formed bondages. Therefore, near infrared reflectance spectroscopy (NIRS) is presented as a rapid alternative to monitor the interaction of glutathione and oxytocin, simulating physiological conditions. Thereby, glutathione can act as a nucleophile with oxytocin forming four new conjugates via a disulphide bondage. Liquid chromatography coupled to UV (LC-UV) and mass spectrometry via an electrospray ionisation interface (LC-ESI-MS) resulted in a 82% and a 78% degradation of oxytocin at pH 3 and a 5% and a 7% degradation at pH 6.5. Capillary electrophoresis employing UV-detection (CE-UV) showed a 44% degradation of oxytocin. LC and CE in addition to the NIRS are found to be authentic tools for quantitative analysis. Nevertheless, NIRS proved to be highly suitable for the detection of newly formed conjugates after separating them on a thin layer chromatography (TLC) plate. The recorded fingerprint in the near infrared region allows for a selective distinct qualitative identification of conjugates without the need for expensive instrumentation such as quadrupole or MALDI-TOF mass spectrometers. The performance of the established NIRS method is compared to LC and CE; its advantages are discussed in detail.     

High-performance liquid chromatographic separation of heparin-derived oligosaccharides

Heparin has been enzymatically depolymerized with heparinase (heparin lyase (EC 4.2.2.7)) and then separated into di-, tetra-, hexa-, octa-, and decasaccharide mixtures by low-pressure gel-permeation chromatography (GPC). These sized mixtures were resolved by strong anion-exchange (SAX) HPLC into multiple components. The fractions from the SAX-HPLC were collected and characterized for size by GPC-HPLC and sulfate content by ion chromatography. This study provides detailed methodology for the separation of larger and more highly sulfated oligosaccharides than previously reported. It describes the first use of ion chromatography for the accurate determination of the sulfate content of heparin oligosaccharides, a method which can also be applied to heparin and other glycosaminoglycans.     

Application of liquid chromatographic method with fluorescence detection for the determination of triclabendazole in tablets and biological fluids

A simple and rapid liquid chromatographic method was developed and validated for the determination of triclabendazole with high accuracy and precision within 6 min. Good chromatographic separation was achieved using a CLC Shim‐pack C₈ (250 × 4.6 mm, 5 µm particle size) using the mobile phase containing a mixture of 0.02 m phosphate buffer and methanol with a ratio of (20 : 80 v/v) at pH 4.0 was pumped at a flow rate of 1.2 mL/min with fluorescence detection for the first time at 338 nm after excitation at 298 nm. Losartan potassium was used as an internal standard. The method showed good linearity in the ranges of 0.05–2.0 µg/mL with limits of detection and quantification of 14.1 and 42.6 ng/mL, respectively. The suggested method was successfully applied for the analysis of triclabendazole in tablets. The high sensitivity of the method enabled the determination of the studied drug in spiked human plasma with mean percentage of recoveries of 99.79 ± 5.09. Statistical evaluation of the data was performed according to ICH Guidelines. Copyright © 2013 John Wiley & Sons, Ltd.     

Limits of detection for the determination of mono- and dicarboxylic acids using gas and liquid chromatographic methods coupled with mass spectrometry

The chromatographic separation and instrumental limits of detection (LODs) were obtained for a broad range of C(1)-C(18) monocarboxylic (MCAs) and C(2)-C(14) dicarboxylic acids (DCAs) employing either chemical derivatization followed by gas chromatography-mass spectrometry and flame ionization detection (GC-MS/FID) or direct analysis with liquid chromatography high resolution MS and tandem MS (LC-MS). Suitability, efficiency and stability of reaction products for several derivatization agents used for esterification (BF(3)/butanol), and trimethysilylation, including trimethylsilyl-N-N-dimethylcarbamate (TMSDMC) and N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) were evaluated. The lowest limits of detection for the majority of compounds below 10 pg (with the exception of acetic acid) were obtained for derivatization with BF(3)/butanol followed by GC-MS in the total ion current (TIC) mode. Further improvements were achieved when applying either selected ion monitoring (SIM), which decreased the LODs to 1-4 pg or a combination of SIM and TIC (SITI) (2-5 pg). GC-FID provided LODs comparable to those obtained by GC-MS TIC. Both trimethylsilylation (followed by GC-MS) and direct LC-MS/MS analysis yielded LODs of 5-40 pg for most of the acids. For volatile acids the LODs were higher, e.g., 25 and 590 ng for TMSDMC and BSTFA derivatized formic acid, respectively, whereas the LC-MS methods did not allow for the analysis of formic acid at all.     

Rapid characterization of biotherapeutic proteins by size-exclusion chromatography coupled to native mass spectrometry

High-molecular weight aggregates such as antibody dimers and other side products derived from incorrect light or heavy chain association typically represent critical product-related impurities for bispecific antibody formats.

In this study, an approach employing ultra-pressure liquid chromatography size-exclusion separation combined with native electrospray ionization mass spectrometry for the simultaneous formation, identification and quantification of size variants in recombinant antibodies was developed. Samples exposed to storage and elevated temperature(s) enabled the identification of various bispecific antibody size variants. This test system hence allowed us to study the variants formed during formulation and bio-process development, and can thus be transferred to quality control units for routine in-process control and release analytics. In addition, native SEC-UV/MS not only facilitates the detailed analysis of low-abundant and non-covalent size variants during process characterization/validation studies, but is also essential for the SEC-UV method validation prior to admission to the market.     

Use of mathematically enhanced spectral analysis and spectral contrast techniques for the liquid chromatographic and capillary electrophoretic detection and identification of pharmaceutical compounds

The use of mathematically enhanced ultraviolet/visible (UV/VIS) absorbance spectral analysis and spectral contrast software techniques in high performance liquid chromatography (HPLC) and micellar electrokinetic capillary electrophoresis (MECC) as an aid for the determination of peak homogeneity, identification, and tracking during method development was investigated. Various structurally similar pharmaceutical compounds, and compounds present as either cis/trans isomers, diastereomers, or enantiomers were used as test compounds to probe the limits of this technique. Two tricyclic antidepressants, nortriptyline and imipramine, were employed to study the effects of HPLC mobile phase composition and pH on the ability to identify and track peaks during method development. It was found that method changes altered the spectral matches used for identification, but not enough to cause incorrect peak identification. It was also shown using HPLC that the cis/trans isomers of doxepin and the diastereomers ephedrine and pseudoephedrine could be distinguished. The mathematically enhanced spectral analysis and spectral contrast software techniques were also employed with MECC. Peaks tracking during method development as pH and the concentration of surfactant changes is shown for a separation of various penicillin type antibiotics. It was shown that during chiral MECC (CMECC) analyses ephedrine/pseudoephedrine diastereomers as well as ephedrine enantiomers could be distinguished. The determination of enantiomers is possible in CMECC since enantiomers are eluted as diastereomeric complexes, as opposed to HPLC where they are eluted in their native state. © 1996 Wiley-Liss, Inc.