Overview about methods for the separation of therapeutic proteins showing the frequency of their application and recommended reviews.
Abstract
A characteristic of many proteoforms, derived from a single gene, is their similarity regarding the composition of atoms, making their analysis very challenging. Many overexpressed recombinant proteins are strongly associated with this problem, especially recombinant therapeutic glycoproteins from large-scale productions. In contrast to small molecule drugs, which consist of a single defined molecule, therapeutic protein preparations are heterogenous mixtures of dozens or even hundreds of very similar species. With mass spectrometry, currently high-quality spectra of intact proteoforms can be obtained only, if the complexity of the mixture of individual proteoform-ions, entering the gas phase at the same time is low. Thus, prior to mass spectrometric analysis, an effective separation is required for getting fractions with a low number of individual proteoforms. This is especially true not only for recombinant therapeutic proteins, because of their huge heterogeneity, but also relevant for top-down proteomics. Purification of proteoforms is the bottleneck in analyzing intact proteoforms with mass spectrometry. This review is focusing on the current state of the art, especially of liquid chromatography for preparing proteoforms for mass spectrometric top-down analysis. The topic of therapeutic proteins has been chosen, because this group of proteins is most challenging regarding their proteoform analysis.
Keywords
- proteoforms
- top-down mass spectrometry
- therapeutic proteins
- liquid chromatography
- protein purification parameter screening
- displacement chromatography
1. Introduction
The analysis of proteoforms, often also termed protein species or isoforms, is the next level in proteomics. The first comprehensive definition of this subgroup of proteins was published by Jungblut et al. [1] and Schlüter et al. [2], using the term “protein species”. In 2013, Smith and Kelleher [3] introduced the term “proteoform”, which today is widely accepted in the community of proteomics experts. The concept of “proteoform” is nearly identical with the concept of “protein species”. The only difference is that the proteoform concept is gene-centric and the protein-species-concept is chemistry-centric.
For developing methods for comprehensive analysis of proteoforms, the group of therapeutic proteins is a suitable training area. Therapeutic proteins are known to be rich in the number of proteoforms. Although a therapeutic protein product is containing only trace amounts of impurities like host cell proteins, which are difficult to detect because of their very low concentration, the analysis of their proteoforms is very challenging because of their large number, their similarity and their low concentration compared to the main proteoform.
2. Analysis of proteoforms: challenges
The most common method in proteomics is the bottom-up or shotgun approach. It relies on the proteolytic cleavage of proteins by proteases like trypsin. The resulting peptide mixture is subjected to liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) analysis. Proteins are identified from the LC–MS/MS data by comparing the peptide fragment spectra against in-silico fragment spectra generated from a protein database [4]. As a rule of thumb, a protein is claimed to be identified, if at least two unique peptides are identified representing parts of the sequence. Thus, often a sequence coverage of 100% is not obtained. Consequently, if this is the case, it can be only stated that a product or several products (proteoforms) of a defined gene has been identified. No information about the identity of the underlying proteoform is obtained. It can even be assumed that the identified tryptic peptides may be products of several different proteoforms. For the characterization of a therapeutic protein, bottom-up proteomics is a standard method. The signals in the LC–MS chromatograms represent tryptic peptides of all proteoforms of the therapeutic protein. A defined tryptic peptide, which is present in all proteoforms, will form one single monoisotopic signal. Its signal intensity represents the sum of this peptide from the different species. The presence of an individual proteoform only can be detected, if this proteoform will yield a tryptic peptide, a defined phosphor-peptide, which is unique for this proteoform. However, it cannot be excluded, that there are several proteoforms containing that peptide. As a result, bottom-up proteomics is helpful for getting LC–MS chromatograms which can be used as fingerprints of a therapeutic protein, but will give no information about the number and composition of proteoforms within the therapeutic protein product. The detection of a low abundant proteoform is especially difficult, since a unique tryptic peptide of such a proteoform is present in a low amount and thereby the signal in a bottom-up proteomics LC–MS chromatogram will have a low intensity. Thus, if the detection of different proteoforms is of interest, top-down mass spectrometry (TDMS) is the method of choice, because it utilizes the intact proteoform for analysis instead of proteolytic peptides.
For performing a TDMS analysis, a purified individual intact proteoform is transferred into the MS. From the MS spectrum of the intact ions, the molecular weight can be determined. Various techniques are available for fragmentation of the intact proteoform such as HCD, CID, ETD, ETHcD, ECD, UVPD and IRMPD, yielding different types for fragments, which complement each other [5]. After fragmentation, the proteoform can be identified by interpreting the fragment spectrum. There are several software tools available for analyzing the TDMS intact data [6, 7, 8]. The review of Schaffer et al. is recommended as an introduction into TDMS [9]. Robust protocols for mass analysis of intact proteins with TDMS were recently published by Donnelly et al. [10]. TDMS is requiring sample mixtures of low complexity for obtaining high quality spectra of proteoforms. Aebersold et al. estimated the number of proteoforms being present in the human organism in the range of approximately a billion [11]. Thus, very efficient purification steps prior to the TDMS are required to tackle the huge number of individual proteoforms in cells and tissues of body fluids. Beside the excessive number of individual proteoforms, their dynamic range is a further challenge.
3. Analysis of proteoforms of recombinant therapeutic proteins: challenges
Similar challenges are associated with recombinant therapeutic proteins. The importance of therapeutic proteins has been continually increasing over the past years [12, 13]. Currently, several types of therapeutic proteins [14] are available in the market including monoclonal antibodies (mAbs), erythropoietin (EPO), insulin, human growth hormone and many more. Therapeutic proteins market is dominated by the monoclonal antibodies with sales of approximately $123 billion in 2017 and will be seen increasing with the upcoming biosimilar market [13]. Therapeutic proteins possess several advantages over small molecule drugs due to their higher specificity towards drug targets, which are in most cases also proteins [15]. This makes therapeutic proteins able to target specific key steps in disease pathology [16].
This group of man-made proteins has presumably a significantly higher number of proteoforms per gene than proteoforms per gene
More common than severe side effects is the phenomenon that , showing even small differences in their composition of atoms compared with the target species, make the species less potent than the target species. For example, deamidation, causing a + 1 Da shift of the molecular weight, can decrease the efficacy of a therapeutic protein [31], as observed with recombinant human interleukin (rhIL)-15 [32]. Deamidation converts asparagine or glutamine to aspartic acid or glutamic acid, respectively. As a result, the polar, uncharged amides are changed into negatively charged carboxylic acids, impacting protein surface-charge density and surface hydrophobicity, thereby explaining the change of the efficacy of a therapeutic protein. Deamidation of asparagine can occur spontaneously at physiological pH of 7.4 [32]. A further important modification of proteins is the disulfide bond (S-S), which is formed by the oxidation of thiol groups (SH) between two cysteine residues resulting in a covalent bond [33], which is decreasing the molecular weight of a protein by 2 Da. Disulfide-bonds have an impact on protein stability as well as on activities [33]. Du et al. stated that during the manufacturing process, extensive reduction of antibodies has been observed after harvest operation or Protein A affinity chromatography and multiple process parameters correlate to the extent of the reduction [34]. The topic “disulfide bonds of therapeutic proteins” is in depth discussed by Lakbub et al. [35].
More details about sources and effects of microheterogeneity are described in the excellent reviews of Beyer [36] and Ambrogelly [37].
4. Separation of proteoforms of therapeutic proteins
4.1 Separation of proteoforms of therapeutic proteins with liquid chromatography
Liquid chromatography (LC) is the most common for purification and fractionation of therapeutic proteins [37]. The proteoforms are either separated by size-exclusion (SEC), making use of different path lengths through chromatographic particles related to the size of the proteins, or by adsorption chromatography. The latter is applying the principle of separation of molecules by their different velocities during crossing a column filled with chromatographic particles. The velocities are proportional to the affinities of the molecules towards the stationary phase of the stationary phase. Depending on the chemistry of the functional groups of the stationary phase, different forms of liquid chromatography are possible based on adsorption to the stationary phase, highlighted in bold in Table 1.
Separation method | Hits of the PubMed search: monoclonal recombinant antibody OR therapeutic-proteins OR biotherapeutics AND “name of the separation method: left column” | Hits after adding filter: “AND (isoform OR variant OR species OR proteoform)” | Review |
---|---|---|---|
Affinity chromatography (AF) | 1046 | 189 | [45, 100] |
Anion exchange chromatography (AEC) | 80 | 20 | [101, 102] |
Cation exchange chromatography (CEX) | 56 | 23 | [49, 103] |
Hydroxyapatite chromatography (HAP) | 6 | 1 | [104] |
Hydrophobic interaction chromatography (HIC) | 46 | 10 | [39] |
Hydrophilic interaction chromatography (HILIC) | 8 | 3 | [51, 52] |
Immobilized metal affinity chromatography (IMAC) | 59 | 5 | [105, 106] |
Mixed mode chromatography (MM) | 10 | 0 | [59] |
Reversed phase chromatography (RP) | 170 | 41 | [107] |
Size exclusion chromatography (SEC) | 973 | 142 | [108] |
Liquid chromatography (LC) | 1969 | 308 | [109] |
Two dimensional liquid chromatography (2D-LC) | 11 | 2 | [110, 111] |
Capillary electrophoresis (CE) | 151 | 31 | [112] |
Two dimensional electrophoresis (2DE) | 12 | 4 | [38, 113] |
Table 1 is giving an overview about the different types of separation methods and their frequency of application with a focus on therapeutic proteins and in addition with respect to proteoforms. The numbers of column 2 compared with column 3 clearly show that the topic of proteoforms is not yet addressed very often. The selected reviews will give deeper insights into the different separation methods.
Mixed mode chromatography (MM) is performed with stationary phases which consist of at least two different functional groups [59], like hydroxy apatite (see above). Consequently, a MM material offers two or more types of chromatography. HAP is combining anion exchange (AEX), cation exchange (CEX) and IMAC. Also, with SEC mixed mode chromatography is possible, as described by Schlüter et al. [60]. In that study the electrostatic interaction induced by anionic sugars, which are part of a dextran polymer, were used to separate vanillylmandelic acid, glycine and phenylalanine from each other with a SEC column, which is usually applied for the separation of proteins in the range of 10–100 kDa. Mixed mode chromatography is not very often described for the chromatography of therapeutic proteins (Table 1), but it has a huge potential for the separation of proteoforms. For successful separations a rational screening of appropriate parameters is recommended.
The major concern in the use of RPLC for protein separations is the presence of organic solvents, which may precipitate proteins. Since precipitation will occur on the column, it is very difficult to recognize. In the case of proteoforms, it can be assumed that some may be more prone to precipitation than others. As a result, the chromatogram, in which signals from some but not all proteoforms are present, may be misinterpreted since the chromatogram is giving no information about the proteoforms which got lost by precipitation. TDMS protocols often apply RPLC for the analysis of proteoforms, because those species, which elute, are present in a liquid, which is optimal for electrospray ionization (ESI). Because of the problem with precipitation of proteins in RPLC in all TDMS approaches the question is how representative the TDMS chromatogram is regarding the original composition of proteoforms or vice versa how many proteoforms got lost during RPLC.
4.2 Separation of proteoforms of therapeutic proteins with capillary electrophoresis
Compared with liquid chromatography, capillary electrophoresis (CE) offers better resolving power. CE techniques such as capillary zone electrophoresis (CZE), capillary gel electrophoresis (CGE) and capillary isoelectric focusing (CIEF) have been adapted for the separation and characterization of proteins [90, 91]. These are basic techniques routinely used for quality control [91]. With CGE, the size of proteins is characterized, while in CIEF, proteins are separated according to their isoelectric point (pI). CIEF is using pH gradients formed by carrier ampholytes in a capillary [92]. It is important to note that pH plays a major role in CZE and should be well maintained [93]. Considerable protein adsorption must be considered when performing CIEF and CZE. The interaction of the analytes with the surface of the capillary may compromise the resolution, peak widths and shapes when using conventional bare fused-silica capillaries. Minimizing adsorption can be done by using better coating material or using reagents that reduce adsorption [94]. A penetrated surface layer protein A from bacteria was reported as capillary coating. The coating could be used for over 100 injections without loss of separation performance [95]. Another study reported that adsorption still happened when using LPA-coated capillary [96].
CZE and CIEF are more often used for separations of charge variants induced by C-terminal lysine truncation, N-terminal pyroglutamate formation, sialylation and deamidation [97].
The direct coupling of CE with MS is technically challenging regarding the CE-MS interface [98]. A study demonstrated a successful attempt to directly couple CIEF with mass spectrometry for characterization of transtuzumab, bevacizumab, cetuzimab and infliximab by optimizing the reagent, liquid composition and enhanced sample mixture by glycerol to reduce non-CIEF electrophoretic mobility and band broadening [99]. A CZE method was developed for the intact analysis of recombinant human interferon-β1 (rhIFN-β1). The charged species due to deamidation and sialylation were sufficiently separated. In contrast to dynamic polymeric coatings, such as polybrene or hydroxypropyl-methylcellulose, they covalently coated the bare-fused silica capillary with cross-linked polyethyleneimine (CPEI) to get positively charged surface, thus reducing the possibility of protein interaction with the coating. They then coupled this CZE to ESI-MS/MS and identified 138 proteoforms, of which, 55 were quantified.
For the in-depth characterization of the composition of proteoforms of a therapeutic protein CE online-coupled to MS is a good option, if prior to the CE, the mixture of proteoforms has already been fractionated by LC using separation mechanisms orthogonal to the CE separation mechanism.
5. Conclusion
A huge progress has been made in the field of TDMS, allowing the identification and comprehensive analysis of the composition of atoms of proteoforms, especially if they are smaller than 30 kDa. TDMS analysis of larger proteoforms still is more challenging. However, until today the most critical point is the purification of a proteoform towards near homogeneity or at least the significant reduction of complexity of the sample, which is desorbed and ionized into a tandem mass spectrometer for TDMS. A low complexity of the composition of a protein mixture entering the MS still is mandatory for getting high quality spectra. Thus, efficient separation methods are needed for obtaining fractions with low complexity. For developing strategies for separating proteoforms, therapeutic proteins are well suited, however challenging because of their heterogeneity. In depth separation of the proteoforms of a therapeutic protein requires the combination of fractionation techniques based on orthogonal mechanisms. In addition, the combination of gradient chromatography and displacement chromatography will add further opportunities for successful separations.
Acknowledgments
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No [765502], A4B project.
Abbreviations
AEX | anion exchange |
ADCs | antibody-drug-conjugates |
CE | capillary electrophoresis |
CGE | capillary gel electrophoresis |
CIEF | capillary isoelectric focusing |
CZE | capillary zone electrophoresis |
CEX | cation exchange |
CID | collision-induced dissociation |
ECD | electron capture dissociation |
ETD | electron transfer dissociation |
ETHcD | electron transfer higher energy collisional dissociation |
ESI | electrospray ionization |
GE | gradient elution |
HCD | higher energy collisional dissociation |
HAP | hydroxyapatite-chromatography |
HILIC | hydrophilic interaction chromatography |
HIC | hydrophobic interaction chromatography |
IMAC | immobilized metal-affinity-chromatography |
IRMPD | infrared multiple photon dissociation |
IEX | ion exchange chromatography |
LC | liquid chromatography |
LC–MS/MS | liquid chromatography coupled to tandem mass spectrometry |
MS | mass spectrometry |
mAbs | monoclonal antibodies |
PPS | protein-purification parameter screening system |
rhIL | recombinant human interleukin |
rTP | recombinant therapeutic protein |
RPLC | reversed phase liquid chromatography |
SEC | size exclusion chromatography |
TDMS | top-down mass spectrometry |
UVPD | ultraviolet photodissociation |
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