Primary Sequence Confirmation of a Protein Therapeutic Using Top Down MS/MS and MS(3).

Mass spectrometry has gained widespread acceptance for the characterization of protein therapeutics as a part of the regulatory approval process. Improvements in mass spectrometer sensitivity, resolution, and mass accuracy have enabled more detailed and confident analysis of larger biomolecules for confirming amino acid sequences, assessing sequence variants, and characterizing post translational modifications. This work demonstrates the suitability of a combined approach using intact MS and multistage top down MS/MS analyses for the characterization of a protein therapeutic drug. The protein therapeutic granulocyte-colony stimulating factor was analyzed using a Thermo Fusion Tribrid mass spectrometer using a multistage top down MS approach. Intact mass analysis identified the presence of two disulfide bonds based on exact mass shifts while a combined collision induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) MS/MS approach obtained 80% protein sequence coverage. Isolating MS/MS fragments for MS(3) analysis using HCD or CID increased the sequence coverage to 89%. 95% sequence coverage was obtained by reducing human granulocyte-colony stimulating factor (G-CSF) prior to MS/MS and MS(3) analysis to specifically target the residues between the disulfide bonds. The use of this combined intact MS and multistage top down MS approach allows for rapid and accurate determination of the primary sequence of a protein therapeutic drug product.

Modern analytics for naturally derived complex drug substances: NMR and MS tests for protamine sulfate from chum salmon.

This work describes orthogonal NMR and MS tests for the structure and composition of the drug protamine sulfate derived from chum salmon. The spectral response pattern obtained by 1D-(1)H-NMR and MS methods from salmon protamine, a mixture of four predominant peptide chains, is dependent on the amino acid sequence and abundance of each peptide. Thus, an assay was developed based on the ratios of alanine, glycine and arginine amino acid residue NMR peaks (relative to the arginine CδH proton signal) in this mixture that are unique to the salmon source. In addition, MS analysis provided sensitive sequence determination and impurity analysis based on shifts from exact masses. Spectra from protamine sulfate active pharmaceutical ingredient (API) suppliers and from a formulated drug product purchased from the US market were examined. Based on these marketplace survey data, NMR acceptance criteria for chum salmon derived protamine sulfate could be based on the absence of aromatic amino acid signals and on ratios of Ala ßH/Arg δH, Gly αH/Arg δH and Arg αH/Arg δH integrated areas of 2.4 ± 1%, 9.4 ± 3% and 50 ± 5%, respectively. For MS, acceptance criteria based on the presence of specific mass to charge (m/z) ratio peaks (m/z = +8 of 530.455, 540.841, 532.208 and 508.950) could be used for the four major peptides present in the mixture with relative abundances of 17 ± 1%, 31 ± 2%, 27 ± 1% and 25 ± 3%, respectively. The specificity of the combined NMR and MS assay was tested by comparison to data obtained from herring protamine which contains a different mixture of peptides with related amino acid sequences. Both assays were able to clearly distinguish protamine derived from these different natural sources.

Identification of site-specific heterogeneity in peptide drugs using intact mass spectrometry with electron transfer dissociation.

RATIONALE: Protamine sulfate is a peptide drug product consisting of multiple basic peptides. As traditional high-performance liquid chromatography (HPLC) separation methods may not resolve these peptides, as well as any possible peptide-related impurities, a method utilizing top-down mass spectrometry was developed for the characterization of complex peptide drug products, including any low-level impurities, which is described in this study. METHODS: Herring protamine sulfate was used as a model system to demonstrate the applicability of the method. Direct infusion mass spectrometry and tandem mass spectrometry (MS/MS) on a high-resolution, mass accurate instrument with electron transfer dissociation (ETD) were used to identify all the species present in the herring protamine sulfate sample. Identifications were made based on mass accuracy analysis as well as MS/MS fragmentation patterns. RESULTS: Complete sequence coverage of the three abundant herring protamine peptides was obtained using the top-down ETD-MS/MS method, which also identified a discrepancy with the published herring protamine peptide sequences. Additionally, three low-abundance related peptide species were also identified and fully characterized. These three peptides had not previously been reported as herring protamine peptides, but could be related to the published sequences through amino acid additions and/or substitutions. CONCLUSIONS: A method for the characterization of protamine, a complex peptide drug product, was developed that can be extended to other complex peptide or protein drug products. The selectivity and sensitivity of this method improves a regulator's ability to identify peptide impurities not previously observed using the established methods and presents an opportunity to better understand the composition of complex peptide drug products.

Analytical techniques and bioactivity assays to compare the structure and function of filgrastim (granulocyte-colony stimulating factor) therapeutics from different manufacturers.

The FDA has approved more than 100 protein and peptide drugs with hundreds more in the pipeline (Lanthier et al. in Nat Rev Drug Discov 7(9):733-737, 2008). Many of these originator biologic products are now coming off patent and are being manufactured by alternate methods than the innovator as follow-on drugs. Because changes to the production method often lead to subtle differences (e.g., degradation products, different posttranslational modifications or impurities) in the therapeutic (Schiestl et al. in Nat Biotechnol 29(4):310-312, 2011), there is a critical need to define techniques to test and insure the quality of these drugs. In addition, the emergence of protein therapeutics manufactured by unapproved methodologies presents an ongoing and growing regulatory challenge. In this work, high-resolution mass spectrometry was used to determine the presence or absence of posttranslational modifications for one FDA-approved and three foreign-sourced, unapproved filgrastim products. Circular dichroism (CD) was used to compare the secondary structure and probe the temperature stability of these products. Native 2D (1)H,(15)N-heteronuclear singular quantum coherence (HSQC) NMR test was applied to these samples to compare the higher-order structure of the four products. Finally, a cell proliferation assay was performed on the filgrastims to compare their bioactivity, and stressed filgrastim was tested in the bioassay to better understand the effects of changes in protein structure on activity. The results showed that orthogonal approaches are capable of characterizing the physiochemical properties of this protein drug and assessing the impact of structural changes on filgrastim purity and potency.

Structural comparison of two anti-CD20 monoclonal antibody drug products using middle-down mass spectrometry.

Liquid chromatography-mass spectrometry (LC-MS) is an information rich analytical tool that can provide fast, robust and sensitive characterization of protein therapeutics for quality assurance and structural comparison. Herein, structural characterization of two anti-CD20 monoclonal antibodies obtained from two different sources was performed using a middle-down LC-MS strategy to determine if they can be analytically differentiated. Through the use of a specific enzymatic digestion method using IdeS with subsequent LC-MS analysis, we show that the anti-CD20 monoclonal antibody that has been approved by the FDA can be partially characterized and differentiated analytically from an Indian sourced product that lacks FDA approval. In comparison to the FDA-approved product, differential modifications to both the N- and C-termini result in increased charge heterogeneity for the Indian product. In addition, significant differences in the intensities of the observed glycoforms between the two antibodies were detected. While this study assesses only one lot of each of a FDA approved drug product and the Indian sourced drug product, the observed differences may represent process specific fingerprints that could be useful for surveillance purposes.

Influence of N-terminal residue composition on the structure of proline-containing b2+ ions.

To probe the structural implications of the proline residue on its characteristic peptide fragmentation patterns, in particular its unusual cleavage at its C-terminus in formation of a b(2) ion in XxxProZzz sequences, the structures of a series of proline-containing b(2)(+) ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy and fragment ion hydrogen-deuterium exchange (HDX). Five different Xxx-Pro b(2)(+) ions were studied, with glycine, alanine, isoleucine, valine, or histidine in the N-terminal position. The residues selected feature different sizes, chain lengths, and gas phase basicities to explore whether the structure of the N-terminal residue influences the Xxx-Pro b(2)(+) ion structure. In proteins, the proline side chain-to-backbone attachment causes its peptide bonds to be in the cis conformation more than any other amino acid, although trans is still favored over cis. However, HP is the only b(2)(+) ion studied here that forms the diketopiperazine exclusively. The GP, AP, IP, and VP b(2)(+) ions formed from protonated tripeptide precursors predominantly featured oxazolone structures with small diketopiperazine contributions. In contrast to the b(2)(+) ions generated from tripeptides, synthetic cyclic dipeptides VP and HP were confirmed to have exclusive diketopiperazine structures.

Evaluation of intact mass spectrometry for the quantitative analysis of protein therapeutics.

Implementation of modern analytical techniques, such as intact mass spectrometry, may allow for more detailed quality assessments of protein therapeutics. The complexity of the protein therapeutic manufacturing process as well as the sensitivity of these drugs to different storage conditions can lead to the presence of several undesired products, including truncations, degradation products, byproducts, and differentially modified protein variants that are difficult to detect by peptide mapping. Intact mass spectrometry can be used to identify the intact protein composition, inclusive of post-translational modifications (PTMs) but can also generate a chemical fingerprint of the different protein species present in a given sample. In this work, we systematically evaluated the influence of multiple charge states, multiple isotopes per charge state, and operating resolution on the suitability of intact mass spectrometry for quantitative analysis using insulin and somatotropin as model systems. Standard curves could be generated using absolute intensity data or using the relative ratio between the analyte and internal standard. These methods demonstrate the validity of quantitative intact mass spectrometry for the analysis of protein therapeutic drugs, thus providing a foundation for future comparative methods.

Structural influences on preferential oxazolone versus diketopiperazine b(2+) ion formation for histidine analogue-containing peptides.

Studies of peptide fragment ion structures are important to aid in the accurate kinetic modeling and prediction of peptide fragmentation pathways for a given sequence. Peptide b(2)(+) ion structures have been of recent interest. While previously studied b(2)(+) ions that contain only aliphatic or simple aromatic residues are oxazolone structures, the HA b(2)(+) ion consists of both oxazolone and diketopiperazine structures. The structures of a series of histidine-analogue-containing Xxx-Ala b(2)(+) ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy, fragment ion hydrogen-deuterium exchange (HDX), and density functional theory (DFT) calculations to systematically probe the influence of different side chain structural elements on the resulting b(2)(+) ion structures formed. The b(2)(+) ions studied include His-Ala (HA), methylated histidine analogues, including π-methyl-HA and τ-methyl-HA, pyridylalanine (pa) analogues, including 2-(pa)A, 3-(pa)A, and 4-(pa)A, and linear analogues, including diaminobutanoic acid-Ala (DabA) and Lys-Ala (KA). The location and accessibility of the histidine π-nitrogen, or an amino nitrogen on an aliphatic side chain, were seen to be essential for diketopiperazine formation in addition to the more typical oxazolone structure formation, while blocking or removal of the τ-nitrogen did not change the b(2)(+) ion structures formed. Linear histidine analogues, DabA and KA, formed only diketopiperazine structures, suggesting that a steric interaction in the HisAla case may interfere with the complete trans-cis isomerization of the first amide bond that is necessary for diketopiperazine formation.

Evidence of diketopiperazine and oxazolone structures for HA b2+ ion.

Peptide fragmentation can lead to an oxazolone or diketopiperazine b(2)(+) ion structure. IRMPD spectroscopy combined with computational modeling and gas-phase H/D exchange was used to study the structure of the b(2)(+) ion from protonated HAAAA. The experimental spectrum of the b(2)(+) ion matches both the experimental spectrum for the protonated cyclic dipeptide HA (a commercial diketopiperazine) and the theoretical spectrum for a diketopiperazine protonated at the imidazole pi nitrogen. A characteristic band at 1875 cm(-1) and increased abundance of the peaks at 1619 and 1683 cm(-1) indicate a second population corresponding to an oxazolone species. H/D exchange also shows a mixture of two populations consistent with a mixture of b(2)(+) ion diketopiperazine and oxazolone structures.

Performance metrics for evaluating system suitability in liquid chromatography--Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies.

The use of liquid chromatography--mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS(2) acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS.

Direct site-specific glycoform identification and quantitative comparison of glycoprotein therapeutics: imiglucerase and velaglucerase alfa.

Gaucher disease, the most common lysosomal metabolic disorder, can be treated with enzyme replacement therapy (ERT). Recombinant human glucocerebrosidase imiglucerase (Cerezyme(®)), produced in Chinese hamster ovary cells, has been used for ERT of Gaucher disease for 20 years. Another recombinant glucocerebrosidase velaglucerase alfa (VPRIV), expressed in a human fibroblast cell line, was approved by the US Food and Drug Administration in 2010. The amino acid sequence difference at residue 495 of these two products is well documented. The overall N-linked qualitative glycan composition of these two products has also been reported previously. Herein, employing our recently developed approach utilizing isobaric tandem mass tag (TMT) labeling and an LTQ Orbitrap XL electron transfer dissociation (ETD) hybrid mass spectrometer, the site-specific glycoforms of these products were identified with ETD and collision-induced dissociation (CID) spectra. The quantitative comparison of site-specific glycans was achieved utilizing higher-energy collisional dissociation (HCD) spectra with a NanoMate used as both a fraction collector and a sample introduction device. From the trypsin-digested mixture of these two products, over 90 glycopeptides were identified by accurate mass matching. In addition to those previously reported, additional glycopeptides were detected with moderate abundance. The relative amount of each glycoform at a specific glycosylation site was determined based on reporter signal intensities of the TMT labeling reagents. This is the first report of site-specific simultaneous qualitative and quantitative comparison of glycoforms for Cerezyme(®) and VPRIV. The results demonstrate that this method could be utilized for biosimilarity determination and counterfeit identification of glycoproteins.

Rapid screening and structural elucidation of a novel sibutramine analogue in a weight loss supplement: 11-desisobutyl-11-benzylsibutramine.

A novel analogue of sibutramine, 11-desisobutyl-11-benzylsibutramine, has been discovered. During routine ion mobility spectrometry (IMS) screening of a weight loss supplement collected at an US FDA import operation facility an unknown peak was observed. Further analysis of the supplement by liquid chromatography-mass spectrometry (LC-MS) and high resolution mass spectrometry revealed an unknown peak with a relative retention time of 1.04 with respect to sibutramine and a predicted formula of C20H24NCl. In order to elucidate the analogue's structure, it was isolated from the supplement and characterized by tandem mass spectrometry and nuclear magnetic resonance (NMR), which revealed the analogue possessed a benzyl moiety at the 11 position in place of the isobutyl group associated with sibutramine.

Separation and identification of structural isomers by quadrupole collision-induced dissociation-hydrogen/deuterium exchange-infrared multiphoton dissociation (QCID-HDX-IRMPD).

A new approach that uses a hybrid Q-FTICR instrument and combines quadrupole collision-induced dissociation, hydrogen-deuterium exchange, and infrared multiphoton dissociation (QCID-HDX-IRMPD) has been shown to effectively separate and differentiate isomeric fragment ion structures present at the same m/z. This method was used to study protonated YAGFL-OH (free acid), YAGFL-NH(2) (amide), cyclic YAGFL, and YAGFL-OCH(3) (methyl ester). QCID-HDX of m/z 552.28 (C(29)H(38)N(5)O(6)) from YAGFL-OH reveals at least two distributions of ions corresponding to the b(5) ion and a non-C-terminal water loss ion structure. Subsequent IRMPD fragmentation of each population shows distinct fragmentation patterns, reflecting the different structures from which they arise. This contrasts with data for YAGFL-NH(2) and YAGFL-OCH(3), which do not show two distinct H/D exchange populations for the C(29)H(38)N(5)O(6) structure formed by NH(3) and HOCH(3) loss, respectively. Relative extents of exchange for C(29)H(38)N(5)O(6) ions from six sequence isomers (YAGFL, AGFLY, GFLYA, FLYAG, LYAGF, and LFGAY) show a sequence dependence of relative isomer abundance. Supporting action IRMPD spectroscopy data are also presented herein and also show that multiple structures are present for the C(29)H(38)N(5)O(6) species from YAGFL-OH.

Understanding and exploiting Peptide fragment ion intensities using experimental and informatic approaches.

Tandem mass spectrometry is a widely used tool in proteomics. This section will address the properties that describe how protonated peptides fragment when activated by collisions in a mass spectrometer and how that information can be used to identify proteins. A review of the mobile proton model is presented, along with a summary of commonly observed peptide cleavage enhancements, including the proline effect. The methods used to elucidate peptide dissociation chemistry by using both small groups of model peptides and large datasets are also discussed. Finally, the role of peak intensity in commercially available and developmental peptide identification algorithms is examined.