High resolution two-dimensional liquid chromatography coupled with mass spectrometry for robust and sensitive characterization of therapeutic antibodies at the peptide level

Comprehensive Two-Dimensional Liquid Chromatography-High-Resolution Mass Spectrometry for Complex Protein Digest Analysis Using Parallel Gradients

Despite the high gain in peak capacity, online comprehensive two-dimensional liquid chromatography coupled with high-resolution mass spectrometry (LC × LC-HRMS) has not yet been widely applied to the analysis of complex protein digests. One reason is the method's reduced sensitivity which can be linked to the high flow rates of the second separation dimension (2D). This results in higher dilution factors and the need for flow splitters to couple to ESI-MS. This study reports proof-of-principle results of the development of an RPLC × RPLC-HRMS method using parallel gradients (2D flow rate of 0.7 mL min-1) and its comparison to shifted gradient methods (2D of 1.4 mL min-1) for the analysis of complex digests using HRMS (QExactive-Plus MS). Shifted and parallel gradients resulted in high surface coverage (SC) and effective peak capacity (SC of 0.6226 and 0.7439 and effective peak capacity of 779 and 757 in 60 min). When applied to a cell line digest sample, parallel gradients allowed higher sensitivity (e.g., average MS intensity increased by a factor of 3), allowing for a higher number of identifications (e.g., about 2600 vs 3900 peptides). In addition, reducing the modulation time to 10 s significantly increased the number of MS/MS events that could be performed. When compared to a 1D-RPLC method, parallel RPLC × RPLC-HRMS methods offered a higher separation performance (FHWH from 0.12 to 0.018 min) with limited sensitivity losses resulting in an increase of analyte identifications (e.g., about 6000 vs 7000 peptides and 1500 vs 1990 proteins).

Liquid-phase separations coupled with ion mobility-mass spectrometry for next-generation biopharmaceutical analysis

INTRODUCTION

The pharmaceutical industry continues to expand its search for innovative biotherapeutics. The comprehensive characterization of such therapeutics requires many analytical techniques to fully evaluate critical quality attributes, making analysis a bottleneck in discovery and development timelines. While thorough characterization is crucial for ensuring the safety and efficacy of biotherapeutics, there is a need to further streamline analytical characterization and expedite the overall timeline from discovery to market.

AREAS COVERED

This review focuses on recent developments in liquid-phase separations coupled with ion mobility-mass spectrometry (IM-MS) for the development and characterization of biotherapeutics. We cover uses of IM-MS to improve the characterization of monoclonal antibodies, antibody-drug conjugates, host cell proteins, glycans, and nucleic acids. This discussion is based on an extensive literature search using Web of Science, Google Scholar, and SciFinder.

EXPERT OPINION

IM-MS has the potential to enhance the depth and efficiency of biotherapeutic characterization by providing additional insights into conformational changes, post-translational modifications, and impurity profiles. The rapid timescale of IM-MS positions it well to enhance the information content of existing assays through its facile integration with standard liquid-phase separation techniques that are commonly used for biopharmaceutical analysis.

Reversed HILIC Gradient: A Powerful Strategy for On-Line Comprehensive 2D-LC

The aim of the present work is to evaluate the possibilities and limitations of reversed hydrophilic interaction chromatography (revHILIC) mode in liquid chromatography (LC). This chromatographic mode consists of combining a highly polar stationary phase (bare silica) with a gradient varying from very low (1-5%) to high (40%) acetonitrile content (reversed gradient compared to HILIC). The retention behavior of revHILIC was first compared with that of reversed-phase LC (RPLC) and HILIC using representative mixtures of peptides and pharmaceutical compounds. It appears that the achievable selectivity can be ranked in the order RPLC > revHILIC > HILIC with the two different samples. Next, two-dimensional liquid chromatography (2D-LC) conditions were evaluated by combining RPLC, revHILIC, or HILIC with RPLC in an on-line comprehensive (LC × LC) mode. evHILIC × RPLC not only showed impressive performance in terms of peak capacity and sensitivity, but also provided complementary selectivity compared to RPLC × RPLC and HILIC × RPLC. Indeed, both the elution order and the retention time range differ significantly between the three techniques. In conclusion, there is no doubt that revHILIC should be considered as a viable option for 2D-LC analysis of small molecules and also peptides.

Theoretical and practical comparison of RPLC and RPLC × RPLC: how to consider dilution effects and sensitivity in addition to separation power?

The objective of this work was to provide an unbiased comparison of one-dimensional reversed-phase liquid chromatography (1D-RPLC) and comprehensive two-dimensional RPLC (RPLC × RPLC), through calculations and experimental verifications. For this purpose, various quality descriptors were evaluated, including peak capacity, analysis time, dilution factor, number of runs in the second dimension, and injection volume. The same strategy was applied to small pharmaceuticals and peptides. Whatever the analysis time between 30 and 200 min, short columns of only 30 × 2.1 mm packed with sub-2-µm particles should be selected in both dimensions of the 2D-LC setup to obtain the best compromise in terms of peak capacity and sensitivity. The peak capacity in RPLC × RPLC vs. RPLC was significantly improved for analysis times beyond 5 min. However, extra-column volume located after the second-dimension column was found to be particularly critical for peptides, and up to 50% lower peak capacity was observed with MS vs. UV detection. Contrary to common belief, higher dilution is not always observed in RPLC × RPLC. With adequate analytical conditions, better sensitivity (in theory fivefold and in practice three- to fivefold) could be achieved in RPLC × RPLC compared to 1D-RPLC, regardless of the analysis time.

Strategies to circumvent the solvent strength mismatch problem in online comprehensive two-dimensional liquid chromatography

On-line comprehensive two-dimensional liquid chromatography is a powerful technique for the separation of highly complex samples. Due to the addition of the second dimension of separation, impressive peak capacities can be obtained within a reasonable analysis time compared to one-dimensional liquid chromatography. In online comprehensive two-dimensional liquid chromatography, the separation power is maximized by selecting two separation dimensions as orthogonal as possible, which most often requires the combination of different mobile phases and stationary phases. The online transfer of a given solvent from the first dimension to the second dimension may cause severe injection effects in the second dimension, mostly due to solvent strength mismatch. Those injection effects may include peak broadening, peak distortion, peak splitting or breakthrough phenomenon. They are often found to reduce significantly the peak capacity and the peak intensity. To overcome such effects, arising specifically in online comprehensive two-dimensional liquid chromatography, different methods have been developed over the years. In this review, we focused on the most recently reported ones. A critical discussion, supported by a theoretical approach, gives an overview of their advantages and drawbacks.

Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase-Reversed Phase Liquid Chromatography High-Resolution Mass Spectrometry for Metaproteomics of Environmental and Microbiome Samples

Metaproteomics is a powerful analytical approach that can assess the functional capabilities deployed by microbial communities in both environmental and biomedical microbiome settings. Yet, the mass spectra resulting from these mixed biological communities are challenging to obtain due to the high number of low intensity peak features. The use of multiple dimensions of chromatographic separation prior to mass spectrometry analyses has been applied to proteomics previously but can require increased sampling handling and instrument time. Here, we demonstrate an automated online comprehensive active modulation two-dimensional liquid chromatography method for metaproteome sample analysis. A high pH PLRP-S column was used in the first dimension followed by low pH separation in the second dimension using dual modulating C18 traps and a C18 column. This method increased the number of unique peptides found in ocean metaproteome samples by more than 50% when compared to a one-dimension separation while using the same amount of sample and instrument time.

Detailed numerical study of the peak shapes of neutral analytes injected at high solvent strength in short reversed-phase liquid chromatography columns and comparison with experimental observations

We report on a numerical investigation of the different steps in the development of the spatial concentration profiles developing along the axis of a liquid chromatography column when injecting large relative volumes (>10 to 20% of column volume) of analytes dissolved in a high solvent strength solvent band as can be encountered in the second dimension (²D) column of a two-dimensional liquid chromatography (2D-LC) system. More specifically, we made a detailed study of the different retention and the axial band broadening effects leading to the double-headed peak shapes or strongly fronting peaks that can be experimentally observed under certain conditions in 2D-LC. The establishment of these intricate peak profiles is discussed in all its fine, mechanistic details. The effect of the volume of the column, the volume and the shape of the sample band, the retention properties of the analyte and the band broadening experienced by the analytes and the sample solvent are investigated. A good agreement between the simulations and the experimental observations with caffeine and methylparaben injected in acetonitrile/water (ACN/H₂O) mobile phase with different injection volumes is obtained. Save the difference in dwell volume, key features of experimental and simulated chromatograms agree within a few %. The simulations are also validated against a number of simple mathematical rules of thumb that can be established to predict the occurrence of a breakthrough fraction and estimate the amount of breakthrough.

Constant pressure mode of operation in the second dimension of two-dimensional liquid chromatography: A proof of concept

The use of two-dimensional liquid chromatography (2D-LC) continues to grow as the advantages over 1D-LC become increasingly clear in specific application areas, and the number of experienced 2D-LC users increases. As with any technique, however, there is always room for innovation that could improve the performance of 2D-LC. In recent years the technical aspects and potential benefits of a volume-based mode of operation were studied in detail for 1D-LC. The salient features of this approach that are immediately interesting for use in 2D-LC are two-fold. First, the ability to maintain a nominally constant pressure in the second dimension by dynamically adjusting the flow rate to compensate for changes in the viscosity of the fluid in the ²D flow path provides a means to more fully utilize the pressure capability of the pumping system, and accelerates separations in the second dimension (²D). Second, constant pressure operation minimizes physical stress on the system components and the ²D column. In this paper we discuss the aspects of volume-based operation of LC that are particularly relevant to 2D-LC systems. The proof-of-concept experiments illustrate the viability of the constant pressure mode of operation for the second dimension of 2D-LC. In the described separations the throughput improvement is on the order of 10%; this gain will be strongly application-dependent, and may be as large as several tens percent in some cases. Future work will involve a detailed investigation of the impact of the constant pressure mode on robustness of ²D separations.

Multi-dimensional LC-MS: the next generation characterization of antibody-based therapeutics by unified online bottom-up, middle-up and intact approaches

This review presents an overview of current analytical trends in antibody characterization by multidimensional LC-MS approaches.

Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry

Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO₂ fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.

Comparison of Online Comprehensive HILIC × RP and RP × RP with Trapping Modulation Coupled to Mass Spectrometry for Microalgae Peptidomics

In this work, two online comprehensive two-dimensional liquid chromatography platforms, namely Hydrophilic interaction liquid chromatography × Reversed phase (HILIC × RP) and Reversed phase × Reversed Phase (RP × RP) coupled to mass spectrometry, were compared for the analysis of complex peptide samples. In the first dimension, a HILIC Amide and C18 Bioshell peptide (150 × 2.1 mm, 1.7 and 2.0 μm) columns were selected, while, in the second dimension, a short C18 (50 × 3.0 mm, 2.7 μm) Bioshell peptide column was used. Two C18 trapping columns (10 × 3.0 mm, 1.9 μm), characterized by high retention and surface area, were employed as modulation interface in both HILIC × RP and RP × RP methods. The LC × LC platforms were coupled to UV and tandem mass spectrometry detection and tested for the separation and identification of two gastro-intestinal digests of commercial microalgae formulations (Spirulina Platensis and Klamath). Their performances were evaluated in terms of peak capacity, maximum number and properties of identified phycocyanin peptides. Our results showed that the HILIC × RP approach provided the highest peak capacity values (nc HILIC × RP: 932 vs. nc RP × RP: 701) with an analysis time of 60 min, while the RP × RP approach was able to identify a slight higher number of phycocyanin derived peptides (HILIC × RP: 88 vs. RP × RP: 103). These results point out the flexibility and potential of HILIC × RP and RP × RP based on trapping modulation for peptide mapping approaches.