Application of Displacement Chromatography to Online Two-Dimensional Liquid Chromatography Coupled to Tandem Mass Spectrometry Improves Peptide Separation Efficiency and Detectability for the Analysis of Complex Proteomes

Application of sample displacement batch chromatography for fractionation of proteoforms

Fractionation of proteoforms is currently the most challenging topic in the field of proteoform analysis. The need for considering the existence of proteoforms in experimental approaches is not only important in Life Science research in general but especially in the manufacturing of therapeutic proteins (TPs) like recombinant therapeutic antibodies (mAbs). Some of the proteoforms of TPs have significantly decreased actions or even cause side effects. The identification and removal of proteoforms differing from the main species, having the desired action, is challenging because the difference in the composition of atoms is often very small and their concentration in comparison to the main proteoform can be low. In this study, we demonstrate that sample displacement batch chromatography (SDBC) is an easy-to-handle, economical, and efficient method for fractionating proteoforms. As a model sample a commercial ovalbumin fraction was used, containing many ovalbumin proteoforms. The most promising parameters for the SDBC were determined by a screening approach and applied for a 10-segment fractionation of ovalbumin with cation exchange chromatography resins. Mass spectrometry of intact proteoforms was used for characterizing the SDBC fractionation process. By SDBC, a significant separation of different proteoforms was obtained.

Mass-to-Charge Ratio Set Matching: A Novel and Efficient Compound Identification Method

Background

GC–MS is a powerful tool for component analysis of unknown compounds, especially in the fields of analytical chemistry and detection of biological samples. To effectively identify compounds in GC–MS, one of the most important ways is to use a matching algorithm to compare the similarity between the reference spectrum and the query spectrum.

Objective

To propose a novel way to improve compound identification accuracy.

Methods

This article proposes a method based on an m/z set match. First of all, select the maximum m/z and the m/z corresponding to the highest peak intensity in a pre-search. Next, employ the space vector model to carry on a refined search in the remaining spectra after the pre-search. Then, distinguish stereoisomers according to the order of the G value.

Results

Compared with the 10 peaks and the method based on an m/z number matching pre-search, the method based on m/z set matching showed higher accuracy and fewer remaining (missing) spectra. Furthermore, the refined search which is based on the m/z set matching method possesses shorter calculation time compared with no pre-search.

Conclusions

The method can reduce the remaining spectra and speed up the identification of compounds.

Highlights

The accuracy is higher, the number of remaining spectra is less, and the computational time is shorter.

Constant-pattern design method for displacement chromatography

Displacement chromatography can be used for the purification of many types of chemicals and biochemicals. In the constant-pattern mode, this method can be used for concentrating and separating various mixtures, leading to higher yields and sorbent productivities than elution chromatography. There are, however, no commercial-scale applications of displacement chromatography. One major barrier is the difficulty in specifying the design variables for reaching a constant-pattern state. A second barrier is that productivity is limited when the feed mixture contains a minority component. In this study, a constant-pattern design method is developed to overcome the first barrier. Theoretical analyses and strategically chosen combinations of key dimensionless groups are used for reducing the multi-dimensional parameter space into a two-dimensional space. Systematic rate model simulations are used to find a general correlation, which divides the two-dimensional space into a transient region and a constant-pattern region. A predictive design method based on the general correlation is developed to find the designs for achieving required product purities and yields with the highest productivities. The design method was shown to increase significantly the productivities or yields for the separations of three binary mixtures. To overcome the second barrier, a multi-zone displacement chromatography method is presented for dividing the separation tasks in multiple zones. For a specific ternary mixture containing a minority component, the sorbent productivity for a two-zone design was 680 times higher than that of a single-column design. This method can be used for developing efficient displacement chromatography processes for purifying a wide range of complex mixtures.

A novel and sensitive method for determination of amisulpride in human plasma by two-dimensional liquid chromatography

A novel and sensitive heart-cutting two-dimensional liquid chromatography with ultraviolet detection method (2D-LC-UV) was developed and validated for determination of amisulpride in human plasma. The 2D-LC system consists of a first dimensional (¹ D) LC column and a middle transfer column as well as a second-dimensional (² D) LC column. After simple protein precipitation, the sample was directly injected into the introduction valve of the 2D-LC system. The ¹ D column, playing a role of primary separation and preconcentration for complex plasma matrices, transferred the targets to the intermediate column. Following capture of targets on the middle column online, the analytes were transferred to the ² D separation column by a six-port valve. The ² D column, avoiding interference from the plasma matrix, completed further separation and quantification. An assistant pump was optimized for primary enrichment as well as final elution in the heart-cutting mode. The analytical time of amisulpride was 7.401 min. The accuracy was between 0.48 and 8.49%, while the intra- and inter-day precisions ranged from 0.9 to 3.1% and from 1.7% to 3.3%, respectively. The linear range of amisulpride was 48.15-2,407.59 ng/ml, while the extraction recovery was 98.7-101.3%. The strategy established in the study, which was successfully applied to therapeutic drug monitoring of amisulpride for routine clinical detection, displays high sensitivity, good repeatability, convenience and low cost.

Development of comprehensive two-dimensional low-flow liquid-chromatography setup coupled to high-resolution mass spectrometry for shotgun proteomics

Bottom-up proteomics provides often small amounts of highly complex samples that cannot be analysed by direct mass spectrometry (MS). To gain a better insight in the sample composition, liquid chromatography (LC) and (comprehensive) two-dimensional liquid chromatography (2D-LC or LC × LC) can be coupled to the MS. Low-flow separations are attractive for HRMS analysis, but they tend to be lengthy. In this work, a low-flow, online, actively modulated LC × LC system, based on hydrophilic-interaction liquid chromatography (HILIC) in the first dimension and reversed-phase liquid chromatography (RPLC) in the second dimension, was developed to separate complex mixtures of peptides. Miniaturization permitted the analysis of small sample amounts (1-5 μg) and direct coupling with micro-ESI MS (1 μL min^-1). All components were focused and automatically transferred from HILIC to RPLC using stationary-phase-assisted active modulation (C18 traps) to deal with solvent-incompatibility or dilution issues. Optimization of the setup was performed for the HILIC columns and the RPLC columns to provide a more efficient separation and higher identification rates than obtained using one-dimensional (1D) LC. A 60% increase in peak capacity was obtained with the 2D setup compared to a 1D-RPLC separation and a 17-34% increase in the number of proteins identified was achieved for the samples analysed (2D-yeast-8280 peptides and 2D-kidney tissue-8843 peptides), without increasing the analysis time (2 h).

Development of an Online 2D Ultrahigh-Pressure Nano-LC System for High-pH and Low-pH Reversed Phase Separation in Top-Down Proteomics

The development of novel high-resolution separation techniques is crucial for advancing the complex sample analysis necessary for high-throughput top-down proteomics. Recently, our group developed an offline 2D high-pH RPLC/low-pH RPLC separation method and demonstrated good orthogonality between these two RPLC formats. Specifically, ultrahigh-pressure long capillary column RPLC separation has been applied as the second dimensional low-pH RPLC separation for the improvement of separation resolution. To further improve the throughput and sensitivity of the offline approach, we developed an online 2D ultrahigh-pressure nano-LC system for high-pH and low-pH RPLC separations in top-down proteomics. An online microtrap column with a dilution setup was used to collect eluted proteins from the first dimension high-pH separation and inject the fractions for ultrahigh-pressure long capillary column low-pH RPLC separation in the second dimension. This automatic platform enables the characterization of 1000+ intact proteoforms from 5 μg of intact E. coli cell lysate in 10 online-collected fractions. Here, we have demonstrated that our online 2D pH RP/RPLC system coupled with top-down proteomics holds the potential for deep proteome characterization of mass-limited samples because it allows the identification of hundreds of intact proteoforms from complex biological samples at low microgram sample amounts.

Mass spectrometric analysis of PTM dynamics using stable isotope labeled metabolic precursors in cell culture

Biological organisms represent highly dynamic systems, which are continually exposed to environmental factors and always strive to restore steady-state homeostasis. Posttranslational modifications are key regulators with which biological systems respond to external stimuli. To understand how homeostasis is restored, it is important to study the kinetics of posttranslational modifications. In this review we discuss proteomic approaches using stable isotope labeled metabolic precursors to study dynamics of posttranslational modifications in cell culture.