Advanced tools for molecular characterization of bio-based and biodegradable polymers

Bio-based and biodegradable materials play a vital role in a sustainable and green economy. These materials must exhibit properties that are similar to or better than the properties of oil- or coal-based materials and require sophisticated synthesis technologies and detailed knowledge of structure-property correlations. For comprehensive molecular structure elucidation, advanced analytical methods, including coupled and hyphenated techniques that combine advanced fractionation and information-rich spectroscopic detectors, are an indispensable tool. One important tool for fractionating complex polymers regarding molecular size is size exclusion chromatography. For fractionating polymers with regard to chemical composition, solvent (or temperature) gradient HPLC has been developed. The combination of different liquid chromatography methods in comprehensive two-dimensional HPLC setups is another important tool. Today, a toolbox of HPLC methods is in place that enables the fractionation of complex bio-based and biodegradable polymers according to the most important molecular parameters including molecular size, composition, functionality, and branching. Here, an overview of the different techniques and some major applications is presented. Some representative developments in the field are discussed, and different techniques, experimental protocols, and applications are highlighted.

Technological development of multidimensional liquid chromatography-mass spectrometry in proteome research

Liquid chromatography-mass spectrometry (LC-MS) is the method of choice for high-throughput proteomic research. Limited by the peak capacity, the separation performance of conventional single-dimensional LC hampers the development of proteomics. Combining different separation modes orthogonally, multidimensional liquid chromatography (MDLC) with high peak capacity was developed to address this challenge. MDLC has evolved rapidly since its establishment, and the progress of proteomics has been greatly facilitated by the advent of novel MDLC-MS-based methods. In this paper, we will review the advances of MDLC-MS-based methodologies and technologies in proteomics studies, from different perspectives including novel application scenarios and proteomic targets, automation, miniaturization, and the improvement of the classic methods in recent years. In addition, attempts regarding new MDLC-MS models are also mentioned together with the outlook of MDLC-MS-based proteomics methods.

Automated ion exchange chromatography screening combined with in silico multifactorial simulation for efficient method development and purification of biopharmaceutical targets

Bioprocess development of increasingly challenging therapeutics and vaccines requires a commensurate level of analytical innovation to deliver critical assays across functional areas. Chromatography hyphenated to numerous choices of detection has undeniably been the preferred analytical tool in the pharmaceutical industry for decades to analyze and isolate targets (e.g., APIs, intermediates, and byproducts) from multicomponent mixtures. Among many techniques, ion exchange chromatography (IEX) is widely used for the analysis and purification of biopharmaceuticals due to its unique selectivity that delivers distinctive chromatographic profiles compared to other separation modes (e.g., RPLC, HILIC, and SFC) without denaturing protein targets upon isolation process. However, IEX method development is still considered one of the most challenging and laborious approaches due to the many variables involved such as elution mechanism (via salt, pH, or salt-mediated-pH gradients), stationary phase's properties (positively or negatively charged; strong or weak ion exchanger), buffer type and ionic strength as well as pH choices. Herein, we introduce a new framework consisting of a multicolumn IEX screening in conjunction with computer-assisted simulation for efficient method development and purification of biopharmaceuticals. The screening component integrates a total of 12 different columns and 24 mobile phases that are sequentially operated in a straightforward automated fashion for both cation and anion exchange modes (CEX and AEX, respectively). Optimal and robust operating conditions are achieved via computer-assisted simulation using readily available software (ACD Laboratories/LC Simulator), showcasing differences between experimental and simulated retention times of less than 0.5%. In addition, automated fraction collection is also incorporated into this framework, illustrating the practicality and ease of use in the context of separation, analysis, and purification of nucleotides, peptides, and proteins. Finally, we provide examples of the use of this IEX screening as a framework to identify efficient first dimension (¹D) conditions that are combined with MS-friendly RPLC conditions in the second dimension (²D) for two-dimensional liquid chromatography experiments enabling purity analysis and identification of pharmaceutical targets.

Multiple heart-cutting mixed-mode chromatography-reversed-phase 2D-liquid chromatography method for separation and mass spectrometric characterization of synthetic oligonucleotides

Until today, ion-pair reversed-phase chromatography is still the dominating method for analytical characterization of synthetic oligonucleotides. Its hyphenation with mass spectrometry, however, has some drawbacks such as ion-suppression in electrospray ionization. To overcome this problem, we present in this work a multiple heart-cutting (MHC) two-dimensional liquid chromatography (2D-LC) method with ultra-violet (UV) and electrospray ionization (ESI) mass spectrometry (MS) detection. A reversed-phase/weak anion-exchange (RP/WAX) stationary phase in the first dimension (¹D) provides the selectivity for separation of structurally closely related oligonucleotide sequences and deletions (shortmers), respectively, using a mixed pH/triethylammonium phosphate buffer gradient at constant organic modifier content. Heart cuts of the oligonucleotide peaks are transferred to the second dimension (²D) via a multiple heart-cutting valve which is equipped with two loop decks. The ²D RP column is used for desalting via a diverter valve. Active solvent modulation enables to refocus the oligonucleotide peak into a sharp zone by ²D RP entirely free of non-volatile buffer components and ion-pair agents. Oligonucleotides can thus be sensitively detected by ESI-QTOF-MS under MS-compatible conditions.

Evaluation of the tubing material and physical dimensions on the performance of extraction columns for on-line sample preparation-LC-MS/MS

Nowadays, high analytical throughputs are required considering an increasing demand for faster, simple and improved methods to analyze contaminants in a considerable number of samples. Generally, these compounds are present in complex matrices in contact with a high number of interferents becoming their determination difficult at low concentration. In this context, on-line extraction techniques arose to improve the extraction as well as separation power, while minimizing errors related to human sample manipulation. This paper describes a study regarding the development and optimization of columns used as an extraction device in multidimensional liquid chromatography. The main goals were the evaluation of the material used as column body as well as the investigation of the tube dimensions (internal diameter and length) in the extraction performance. Firstly, several tube materials were tested (steel, fused silica, PEEK, among others) being steel whose reported the best performance and was consequently chose for further studies. The investigation about the effects of the columns physical dimensions revealed a linear relationship between performance and the amount of sorbent utilized as extractive phase. However, when different columns with same amount of sorbent were tested results suggests that both i.d. and lengths play an important role in extraction efficiency. The longest columns with lower internal diameter showed the best results favoring the radial as well as axial analytes diffusion into the extraction column. After evaluation of these column variables, applications were carried out employing several different analytes belonging to various chemical classes and practical utilization, in order to reinforce the versatility as well as the robustness of this proposed study.

Improving deep proteome and PTMome coverage using tandem HILIC-HPRP peptide fractionation strategy

Despite being orthogonal to reverse-phase separation and valuable for posttranslational modification (PTM) pre-enrichment, hydrophilic interaction liquid chromatography (HILIC) has not been widely adopted for large-scale proteomic applications. Here, we first evaluated the performance of HILIC in comparison with the popular high-pH reverse-phase (HPRP) separation, as the first dimension for tryptic peptide fractionation in a shotgun workflow to characterize the complex 293T cell proteome. The data indicated that the complementary nature of HILIC and HPRP for peptide separation was mainly due to different hydrophobicity preferences. Realizing that uncaptured components from one mode can be resolved in the other mode, we then designed and compared two multidimensional separation schemes using HILIC and HPRP in tandem for peptide prefractionation, in terms of identification efficiency and coverage at peptide, protein, and PTM levels. A total of 22,604 and 23,566 peptides corresponding to 4481 and 4436 proteins from 293T cell lysate were detected using HILIC-HPRP- and HPRP-HILIC-based shotgun proteomics workflow, respectively. In addition, without assistance of enrichment techniques, the tandem fractionation methods aided to identify 46 different PTMs from over 10,000 of spectra using blind modification search algorithm. We concluded that HILIC is a valuable alternative option for peptide prefractionation in a large-scale proteomic study, but can be further augmented with the use of a secondary HPRP separation.

Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards

Absolute quantitative strategies are emerging as a powerful and preferable means of deriving concentrations in biological samples for systems biology applications. Method development is driven by the need to establish new-and validate current-protein biomarkers of high-to-low abundance for clinical utility. In this chapter, we describe a methodology involving two-dimensional (2D) reversed-phase liquid chromatography (RPLC), operated under alkaline and acidic pH conditions, combined with multiple reaction monitoring (MRM)-mass spectrometry (MS) (also called selected reaction monitoring (SRM)-MS) and a complex mixture of stable isotope-labeled standard (SIS) peptides, to quantify a broad and diverse panel of 253 proteins in human blood plasma. The quantitation range spans 8 orders of magnitude-from 15 mg/mL (for vitamin D-binding protein) to 450 pg/mL (for protein S100-B)-and includes 31 low-abundance proteins (defined as being <10 ng/mL) of potential disease relevance. The method is designed to assess candidates at the discovery and/or verification phases of the biomarker pipeline and can be adapted to examine smaller or alternate panels of proteins for higher sample throughput. Also detailed here is the application of our recently developed software tool-Qualis-SIS-for protein quantitation (via regression analysis of standard curves) and quality assessment of the resulting data. Overall, this chapter provides the blueprint for the replication of this quantitative proteomic method by proteomic scientists of all skill levels.