Novel liquid-chromatography columns for proteomics research

Combining offline high performance liquid chromatography fractionation of peptides and intact proteins to enhance proteome coverage in bottom-up proteomics

Offline peptide separation (PS) using high-performance liquid chromatography (HPLC) is currently used to enhance liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection of proteins. In search of more effective methods for enhancing MS proteome coverage, we developed a robust method for intact protein separation (IPS), an alternative first-dimension separation technique, and explored additional benefits that it offers. Comparing IPS to the traditional PS method, we found that both enhance detection of unique protein IDs to a similar magnitude, though in diverse ways. IPS was especially effective in serum, which has a small number of extremely high abundance proteins. PS was more effective in tissues with fewer dominating high-abundance proteins and was more effective in enhancing detection of post-translational modifications (PTMs). Combining the IPS and PS methods together (IPS+PS) was especially beneficial, enhancing proteome detection more than either method could independently. The comparison of IPS+PS versus six PS fractionation pools increased total number of proteins IDs by nearly double, while also significantly increasing number of unique peptides detected per protein, percent peptide sequence coverage of each protein, and detection of PTMs. This IPS+PS combined method requires fewer LC-MS/MS runs than current PS methods would need to obtain similar improvements in proteome detection, and it is robust, time- and cost-effective, and generally applicable to various tissue and sample types.

Functionalized monolithic columns: Recent advancements and their applications for high-efficiency separation and enrichment in food and medicine

The chromatographic column is the core of a high-performance liquid chromatography (HPLC) system, and must have excellent separation efficiency and selectivity. Therefore, functional modification materials for monolithic columns have been rapidly developed. This study is a systematic review of the recently reported functionalized monolithic columns. In particular, the study reviews the types of functional monomers under different modification conditions, as well as the separation and detection techniques combined with chromatography, and their development prospects. In addition, the applications of functionalized monolithic columns in food analysis, biomedicine, and the analysis of active ingredient of Chinese herbal medicines in recent years are also discussed. Also reviewed are the functionalized monolithic columns for qualitative and quantitative analysis. It provided a reference for further development and application of organic polymer monolithic columns.

Development and Evaluation of HILIC-type Sorbents Modified with Hydrophilic Copolymers for Solid-phase Extraction

Hydrophilic interaction chromatography (HILIC) has attractive attention for the separation of water-soluble compounds via HPLC. There are, however, few studies on the pretreatment of the HILIC-type solid-phase extraction (SPE) due to the difficulty of obtaining the HILIC-type sorbent. Therefore, the development of HILIC-type sorbents for SPE is essential. In this study, four different hydrophilic copolymers, namely diallylamine-maleic acid copolymer (DAM), diallylamine-acrylamide copolymer (DAA), allylamine-maleic acid copolymer (MAM), and partly methylcarbonylated allylamine acetate copolymer (MAC), were immobilized on glycidyl methacrylate (GMA)-base resin, and their adsorptive properties were evaluated. The results of the physical and adsorptive properties indicated that a balance between the water content of the water-enriched layer on sorbent and the amount of hydrophilic copolymer immobilized on the GMA-base resin was vital for the adsorption in HILIC-type sorbent for SPE.

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.

Development of a reproducible method of analysis of iron, zinc and phosphorus in vegetables digests by SEC-ICP-MS

Vegetables contain iron, zinc and phosphorus as complexes with phytates limiting their availability from a vegetarian diet, meaning non-haem iron deficiency anaemia and zinc deficiency immune malfunction are a risk. Although these elements have been analysed previously in biological fluids and cereal using LC-ICP-MS, there is no method suitable for analysing iron, zinc and phosphorus simultaneously in vegetables because of their complex matrix. In this study, we analysed iron, zinc and phosphorus in cabbage, broccoli, pepper, spinach, kale and rocket after a simulated gastrointestinal digestion using a newly optimised SEC-ICP-MS method. Ammonium nitrate, as the mobile phase, and a suitable rinsing regime, allowed good reproducibility and maintenance of the equipment. The method showed good reproducibility and can be easily adapted to other vegetables, as required.

New platform for simple and rapid protein-based affinity reactions

We developed a spongy-like porous polymer (spongy monolith) consisting of poly(ethylene-co-glycidyl methacrylate) with continuous macropores that allowed efficient in situ reaction between the epoxy groups and proteins of interest. Immobilization of protein A on the spongy monolith enabled high-yield collection of immunoglobulin G (IgG) from cell culture supernatant even at a high flow rate. In addition, immobilization of pepsin on the spongy monolith enabled efficient online digestion at a high flow rate.

Plant responses to ambient temperature fluctuations and water-limiting conditions: A proteome-wide perspective

BACKGROUND

Every year, environmental stresses such as limited water and nutrient availability, salinity, and temperature fluctuations inflict significant losses on crop yields across the globe. Recently, developments in analytical techniques, e.g. mass spectrometry, have led to great advances towards understanding how plants respond to environmental stresses. These processes are mediated by many molecular pathways and, at least partially, via proteome-environment interactions.

SCOPE OF REVIEW

This review focuses on the current state of knowledge about interactions between the plant proteome and the environment, with a special focus on drought and temperature responses of plant proteome dynamics, and subcellular and organ-specific compartmentalization, in Arabidopsis thaliana and crop species.

MAJOR CONCLUSIONS

Correct plant development under non-optimal conditions requires complex self-protection mechanisms, many of them common to different abiotic stresses. Proteome analyses of plant responses to temperature and drought stresses have revealed an intriguing interplay of modifications, mainly affecting the photosynthetic machinery, carbohydrate metabolism, and ROS activation and scavenging. Imbalances between transcript-level and protein-level regulation observed during adaptation to abiotic stresses suggest that many of the regulatory processes are controlled at translational and post-translational levels; proteomics is thus essential in revealing important regulatory networks.

GENERAL SIGNIFICANCE

Because information from proteomic data extends far beyond what can be deduced from transcriptome analysis, the results of proteome studies have substantially deepened our understanding of stress adaptation in plants; this is clearly a prerequisite for designing strategies to improve the yield and quality of crops grown under unfavorable conditions brought about by ongoing climatic change. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Rapid chromatographic determination of caseins in milk with photometric and fluorimetric detection using a hydrophobic monolithic column

Reverse-phase liquid chromatographic methods using a hydrophobic C18 monolithic column and on-line photometric and fluorimetric detection for the determination of the major casein (CN) proteins in milk are presented. The separation of αs1-CN, αs2-CN, β-CN and κ-CN was achieved in only five minutes. Fluorimetric detection enabled better analytical results than photometric detection. Thus, the dynamic ranges of the calibration graphs and detection limits obtained using fluorimetric detection were (mgmL(-)(1)): αs1-CN (0.74-10.0, 0.22), αs2-CN (0.15-10.0, 0.045), β-CN (0.68-10.0, 0.20) and κ-CN (0.21-10.0, 0.06). The analytical features of the photometric method, which does not allow the quantification of β-casein, were (mgmL(-)(1)): αs1-CN (1.5-9.0, 0.45), αs2-CN (1.4-10.0, 0.43) and κ-CN (0.4-9.0, 0.12). Precision data, expressed as relative standard deviation, ranged between 0.6% and 5.3% for the fluorimetric method and between 2.4% and 6.2% for the photometric method. Both methods were applied to the analysis of three different milk samples, obtaining recoveries in the ranges of 86.6-103.2% and 92.0-106.5% using fluorimetric and photometric detection, respectively.

Challenges in the development of bioanalytical liquid chromatography-mass spectrometry method with emphasis on fast analysis

The development of bioanalytical methods has become more and more challenging over the past years due to very demanding requirements in terms of method reliability, sensitivity, speed of analysis and sample throughput. LC-MS/MS has established itself as a method of choice for routine analysis of biological materials. A development of such method consists of several steps including sample preparation and clean-up step, efficient chromatographic separation, sensitive and selective detection of analytes in complex matrices, a choice of convenient data processing and calibration approach and finally method validation. Each of these steps has its own constraints and challenges, which are discussed in detail in this review. Novel and modern approaches in sample preparation, chromatography and detection are especially emphasized. Attention is paid to proper calibration approach and matrix effects that can seriously affect method accuracy and precision.

Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review

With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.

New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications

In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 μm particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources.