Signature peptides of influenza nucleoprotein for the typing and subtyping of the virus by high resolution mass spectrometry

Enhancing saliva diagnostics: The impact of amylase depletion on MALDI-ToF MS profiles as applied to COVID-19

Introduction

Human saliva contains a wealth of proteins that can be monitored for disease diagnosis and progression. Saliva, which is easy to collect, has been extensively studied for the diagnosis of numerous systemic and infectious diseases. However, the presence of amylase, the most abundant protein in saliva, can obscure the detection of low-abundance proteins by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-ToF MS), thus reducing its diagnostic utility.

Objectives

In this study, we used a device to deplete salivary amylase from water-gargle samples by affinity adsorption. Following depletion, saliva proteome profiling was performed using MALDI-ToF MS on gargle samples from individuals confirmed to have COVID-19 based on nasopharyngeal (NP) swab reverse transcription quantitative polymerase chain reaction (RT-qPCR).

Results

The depletion of amylase led to increased signal intensities of various peaks and the detection of previously unobserved peaks in the MALDI-ToF MS spectra. The overall specificity and sensitivity after amylase depletion were 100% and 85.17%, respectively, for detecting COVID-19.

Conclusion

This simple, rapid, and inexpensive technique for depleting salivary amylase can reveal spectral diversity in saliva using MALDI-ToF MS, expose low-abundance proteins, and assist in establishing novel biomarkers for diseases.

25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry

This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.

High resolution mass spectrometry of respiratory viruses: beyond MALDI-ToF instruments for next generation viral typing, subtyping, variant and sub-variant identification

In the wake of the SARS-CoV2 pandemic, a point has been reached to assess the limitations and strengths of the analytical responses to virus identification and characterisation. Mass spectrometry has played a growing role in this area for over two decades, and this review highlights the benefits of mass spectrometry (MS) over PCR-based methods together with advantages of high mass resolution, high mass accuracy strategies over conventional MALDI-ToF and ESI-MS/MS instrumentation. This review presents the development and application of high resolution mass spectrometry approaches to detect, characterise, type and subtype, and distinguish variants of the influenza and SARS-CoV-2 respiratory viruses. The detection limits for the identification of SARS-CoV2 virus variants in clinical specimens and the future uptake of high resolution instruments in clinical laboratories are discussed. The same high resolution mass data can be used to monitor viral evolution and follow evolutionary trajectories.

Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants

Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.

Detection, Mapping, and Proteotyping of SARS-CoV-2 Coronavirus with High Resolution Mass Spectrometry

A high resolution mass spectrometry approach has been applied for the first time to detect and characterize SARS-CoV-2 coronavirus in cell cultured and nasopharyngeal swab specimens. Peptide ions for three of the most abundant structural viral proteins (membrane, nucleocapid, and spike) are detected and assigned directly, by virtue of the high resolution and mass accuracy within the mass maps of whole virus digests, without the need for tandem mass spectrometry (MS/MS). MALDI-MS based approaches offer high sample throughput and speed, compared with those of LC-MS strategies, and detection limits at some 105 copies, or orders of magnitude less with selected ion monitoring, that compete favorably with conventional reverse transcription polymerase chain reaction (RT-PCR) strategies. The detection of signature peptides unique to SARS-CoV-2 coronavirus over those from the influenza virus allows for its unambiguous detection.

A Molecular Immunoproteomics Approach to Assess the Viral Antigenicity of Influenza

New surveillance methods employing mass spectrometry (MS) have been developed to characterize the influenza virus and, by extension, other biopathogens at the molecular level. The structure and antigenicity of protein antigens on the surface of the viral capsid are screened in a single step employing the immunoproteomics MS-based approach. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) coupled to gel electrophoresis is used both to identify viral antigens and screen their antigenicity. Evidence that antigen-antibody complexes, and protein complexes more generally, can survive on conventional MALDI targets has allowed both the primary structure and antigenicity of viral strains to be rapidly screened and protein epitopes to be identified with molecular precision. The approach should aid in future screening of the virus and assist in the development of immunogenic peptide constructs as alternative treatments to vaccination over the whole inactivated virus. The assay adds to the repertoire of mass spectrometric approaches for examining antigen-antibody interactions, in particular, and protein complexes, in general, without the need to immobilize, tag, or recover either component.

Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines

The outbreak of a pandemic influenza H1N1 in 2009 required the rapid generation of high-yielding vaccines against the A/California/7/2009 virus, which were achieved by either addition or deletion of a glycosylation site in the influenza proteins hemagglutinin and neuraminidase. In this report, we have systematically evaluated the glycan composition, structural distribution and topology of glycosylation for two high-yield candidate reassortant vaccines (NIBRG-121xp and NYMC-X181A) by combining various enzymatic digestions with high performance liquid chromatography and multiple-stage mass spectrometry. Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. A total of ~300 glycopeptides were analyzed and manually validated by tandem mass spectrometry. The specific N-glycan structure and topological location of these N-glycans are highly correlated to the spatial protein structure and the residential ligand binding. Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants.

Subtyping of hepatitis C virus with high resolution mass spectrometry

A proteotyping approach using high resolution mass spectrometry has been applied, for the first time, to subtype the hepatitis C virus based upon detection of one or more signature peptides derived from the E1 and E2 envelope glycoproteins. These signature peptides represent conserved peptide segments within these proteins for particular subtypes of the virus that are found to be unique in mass when compared with the theoretical masses for all peptide segments of translated HCV proteins within a specifically constructed database. The successful application of the approach to three different subtypes of the virus (i.e., 1a, 1b and 2b) is demonstrated for protein and whole virus proteolytic digests. The approach has the potential to replace existing PCR-based subtyping by offering a more direct and cost comparable strategy that is not challenged by mixed infection scenarios.

Rapid and generic identification of influenza A and other respiratory viruses with mass spectrometry

The rapid identification of existing and emerging respiratory viruses is crucial in combating outbreaks and epidemics. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and reliable identification method in bacterial diagnostics, but has not been used in virological diagnostics. Mass spectrometry systems have been investigated for the identification of respiratory viruses. However, sample preparation methods were laborious and time-consuming. In this study, a reliable and rapid sample preparation method was developed allowing identification of cultured respiratory viruses. Tenfold serial dilutions of ten cultures influenza A strains, mixed samples of influenza A virus with human metapneumovirus or respiratory syncytial virus, and reconstituted clinical samples were treated with the developed sample preparation method. Subsequently, peptides were subjected to MALDI-TOF MS and liquid chromatography tandem mass spectrometry (LC-MS/MS). The influenza A strains were identified to the subtype level within 3h with MALDI-TOF MS and 6h with LC-MS/MS, excluding the culturing time. The sensitivity of LC-MS/MS was higher compared to MALDI-TOF MS. In addition, LC-MS/MS was able to discriminate between two viruses in mixed samples and was able to identify virus from reconstituted clinical samples. The development of an improved and rapid sample preparation method allowed generic and rapid identification of cultured respiratory viruses by mass spectrometry.

Proteotyping for the rapid identification of influenza virus and other biopathogens

The influenza virus is one of the most deadly infectious agents known to man and has been responsible for the deaths of some hundred million lives throughout human history. The need to rapidly and reliably survey circulating virus strains down to the molecular level is ever present. This tutorial describes the development and application of a new proteotyping approach that harnesses the power of high resolution of mass spectrometry to characterise the influenza virus, and by extension other bacterial and viral pathogens. The approach is shown to be able to type, subtype, and determine the lineage of human influenza virus strains through the detection of one or more signature peptide ions in the mass spectrum of whole virus digests. Pandemic strains can be similarly distinguished from seasonal ones, and new computer algorithms have been written to allow reassorted strains that pose the greatest pandemic risk to be rapidly identified from such datasets. The broader application of the approach is further demonstrated here for the parainfluenza virus, a virus which can be life threatening to children and presents similar clinical symptoms to influenza.

Origins of the reassortant 2009 pandemic influenza virus through proteotyping with mass spectrometry

The application of a proteotyping approach employing high resolution mass spectrometry based is shown to be able to determine the gene origin of all major viral proteins in a triple reassortant pandemic 2009 influenza strain. Key to this approach is the identification of unique swine-host-specific signature and indicator peptides that are characteristic of influenza viruses circulating in North American and Eurasian swine herds in the years prior to the 2009 influenza pandemic. These swine-and human pandemic-specific signatures enable the origins of viral proteins in a clinical virus specimen to be determined and such strains to be rapidly and directly differentiated from other co-circulating seasonal influenza viruses from the same period. The proteotyping strategy offers advantages over traditional RT-PCR-based approaches that are currently the mainstay of influenza surveillance at the molecular level.

Incorporation of a proteotyping approach using mass spectrometry for surveillance of influenza virus in cell-cultured strains

The reemergence of deadly pandemic influenza virus strains has necessitated the development of improved methods for rapid detection and subtyping of influenza viruses that will enable more strains to be characterized at the molecular level. Representative circulating strains of human influenza viruses from primary clinical specimens were grown in cell culture, purified through polyethylene glycol precipitation, proteolytically digested with an endoproteinase, and analyzed and identified by high-resolution mass spectrometry using unique signature peptides that are characteristic of type A H1N1 and H3N2 and type B influenza viruses. This proteotyping approach enabled circulating strains of type A influenza virus to be typed and subtyped, cocirculating seasonal and pandemic H1N1 viruses to be differentiated, and the lineage of type B viruses to be determined through single-ion detection by high-resolution mass spectrometry. Results were obtained using virus titers comparable to those used in reverse transcription (RT)-PCR assays with clinical specimens grown in cell cultures. The methodology represents a more rapid and direct approach than RT-PCR and can be integrated into existing procedures currently used for the surveillance of emerging pandemic and seasonal influenza viruses.

Mass spectrometric approaches to study enveloped viruses: new possibilities for structural biology and prophylactic medicine

This review considers principles of the use of mass spectrometry for the study of biological macromolecules. Some examples of protein identification, virion proteomics, testing vaccine preparations, and strain surveillance are represented. Possibilities of structural characterization of viral proteins and their posttranslational modifications are shown. The authors’ studies by MALDI-MS on S-acylation of glycoproteins from various families of enveloped viruses and on oligomerization of the influenza virus hemagglutinin transmembrane domains are summarized.

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry

A new phylogenetics approach and algorithm with which to chart the evolutionary history of organisms is presented. It utilizes mass spectral data produced from the proteolytic digestion of proteins, rather than partial or complete gene or translated gene sequences. The concept and validity of the approach is demonstrated herein using both theoretical and experimental mass data, together with the translated gene sequences of the hemagglutinin protein of the influenza virus. A comparison of the mass trees with conventional sequenced-based phylogenetic trees, using two separate tree comparison algorithms, reveals a high degree of similarity and congruence among the trees. Given that the mass map data can be generated more rapidly than gene sequences, even when next generation parallel sequencing is employed, mass trees offer new opportunities and advantages for phylogenetic analysis.

Subtyping of influenza neuraminidase using mass spectrometry

A proteotyping approach which employs high resolution mass spectrometry is shown to be able to differentiate all nine neuraminidase subtypes of type A influenza viruses that infect both humans and animals. Conserved sequences among tryptic peptides were identified through alignments of influenza neuraminidase sequences across all subtypes N1-N9 among human and animal hosts. Those that were unique in mass represent signature peptides which, when detected in the mass spectra of an influenza neuraminidase or whole virus digest, enable strains to be subtyped with confidence. The ability to distinguish N1 neuraminidase derived from human H5N1 and H1N1 strains is also demonstrated. The approach provides a more rapid and direct approach with which to subtype the virus than conventional molecular based PCR methods with comparable sensitivity. This should help facilitate a more rapid response in the event of a local epidemic or global pandemic.

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry

BACKGROUND

Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented.

RESULTS

The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. FluShuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. FluResort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain.

CONCLUSIONS

The new FluShuffle and FluResort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk.

Enhanced reliability of avian influenza virus (AIV) and Newcastle disease virus (NDV) identification using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS)

In-solution enzymatic and nonenzymatic digestion methods have been successfully implemented in matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS)-based virus identification, extending to typing/subtyping of deadly influenza viruses. However, these methods are inefficient in obtaining more precise information on surface proteins of myxovirus particles, not only the hemagglutinin and neuraminidase of influenza virus but also the hemagglutinin-neuraminidase of Newcastle disease virus (NDV). Imbalances in viral protein composition cause ion suppression of tryptic fragments from low-abundant target proteins (surface proteins), adversely affecting reproducibility of mass spectra. Additionally, the coexistence of tryptic peptides from several proteins requires sophisticated statistical solutions for precise result interpretations. To circumvent these, we apply detergent-based (gel-free) partitioning of whole viruses into soluble surface proteins and insoluble virus materials, using differential centrifugation. MALDI-TOF or MALDI-TOF/TOF MS was applied to analyze tryptic peptides from separated viral proteins. In this study, we achieved type/subtype of avian influenza virus (AIV) within 5 h, based on 4 major proteins, by significantly reducing ion suppression and signal overlap from various protein sources. Hence, our approach can both yield dependable results and allow Web-based search engines to be directly employed, obviating the need for additional statistical strategy. Additionally, we demonstrate the utility of the method using NDV.

Proteotyping to establish gene origin within reassortant influenza viruses

The application of a rapid and direct proteotyping approach with which to identify the gene origin of viral antigens in a reassortant influenza strain is demonstrated. The reassortant strain, constructed for a vaccine against type A 2009 H1N1 pandemic influenza, contains genes derived from a wild-type pandemic strain (A/California/7/2009) and an egg adapted high-growth strain (denoted NYMC X-157) derived from an earlier A/Puerto Rico/8/34 strain. The proteotyping approach employs modern proteomics methods and high resolution mass spectrometry to correctly establish that the genes of the surface antigens, hemagglutinin and neuraminidase, are derived from the A/California/7/2009 strain while those for nucleoprotein and matrix protein M1 antigens are derived from the NYMC X-157 strain. This is achieved for both gel-separated antigens and those from a whole vaccine digest. Furthermore, signature peptides detected in the mass spectra of the digested antigens enable the engineered reassortant strain to be identified as a type A virus of the H1N1 subtype in accord with earlier studies. The results demonstrate that proteotyping approach provides a more direct and rapid approach over RT-PCR with which to characterize reassortant strains of the influenza virus at the molecular protein level. Given that these strains pose the greatest risk to human and animal health and have been responsible for all human pandemics of the 20th and 21st centuries, there is a vital need for the origins and evolutionary history of these strains to be rapidly established.

Proteotyping to establish the lineage of type A H1N1 and type B human influenza virus

The ability to establish the lineage of type A H1N1 and type B human influenza virus strains using a new proteotyping approach is demonstrated. Lineage-specific signature peptides have been determined for the hemagglutinin antigen of type A H1N1 and type B influenza viruses. The detection of these peptides alone within the high resolution mass spectra of whole antigen digests enables the lineage of the strain to be rapidly and unequivocally assigned. This proteotyping approach complements conventional PCR approaches and should aid in the monitoring of the evolution of the influenza virus in both humans and animals.

Rapid differentiation of seasonal and pandemic H1N1 influenza through proteotyping of viral neuraminidase with mass spectrometry

Signature peptides of the neuraminidase antigen across all common circulating human subtypes of type A and B influenza are identified through the bioinformatic alignment of translated gene sequences. The detection of these peptides within the high-resolution mass spectra of whole antigen, virus, and vaccine digests enables the strains to be rapidly and directly typed and subtyped. Importantly, unique signature peptides for pandemic (H1N1) 2009 influenza are identified and detected that enable pandemic strains to be rapidly and directly differentiated from seasonal type A (H1N1) influenza strains. The detection of these peptides can enable the origins of the neuraminidase gene to be monitored in the case of reassorted strains.

FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data

BACKGROUND

High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assignment of the type and subtype of a given strain. This analysis has, to date, required the manual inspection of mass spectra of whole virus and antigen digests.

RESULTS

A computer algorithm, FluTyper, has been designed and implemented to achieve the automated analysis of MALDI mass spectra recorded for proteolytic digests of the whole influenza virus and antigens. FluTyper incorporates the use of established signature peptides and newly developed naïve Bayes classifiers for four common influenza antigens, hemagglutinin, neuraminidase, nucleoprotein, and matrix protein 1, to type and subtype the influenza virus based on their detection within proteolytic peptide mass maps. Theoretical and experimental testing of the classifiers demonstrates their applicability at protein coverage rates normally achievable in mass mapping experiments. The application of FluTyper to whole virus and antigen digests of a range of different strains of the influenza virus is demonstrated.

CONCLUSIONS

FluTyper algorithm facilitates the rapid and automated typing and subtyping of the influenza virus from mass spectral data. The newly developed naïve Bayes classifiers increase the confidence of influenza virus subtyping, especially where signature peptides are not detected. FluTyper is expected to popularize the use of mass spectrometry to characterize influenza viruses.

Typing of human and animal strains of influenza virus with conserved signature peptides of matrix M1 protein by high resolution mass spectrometry

The use of high resolution mass spectrometry to detect signature peptides within proteolytic digests of the isolated matrix M1 protein, and whole virus digests, for both human and animal strains of influenza is shown to be able to rapidly and reliably type the virus. Conserved sequences for predicted tryptic peptides were identified through alignments of matrix M1 protein sequences across all human, avian and swine strains of the influenza virus. Peptides with unique masses, when compared with those from the in silico digestion of all influenza antigens and those proteins known to contaminate egg grown strains, were identified using the purpose built FluGest algorithm. Their frequency of occurrence within the matrix M1 protein across all type A and type B strains was established with the FluAlign algorithm. The subsequent detection of the signature peptides of matrix M1 protein within proteolytic digests of type A and type B human and avian strains has been demonstrated.

Rapid typing and subtyping of vaccine strains of the influenza virus with high resolution mass spectrometry

The application of high-resolution mass spectrometry to type and subtype strains of the influenza virus within recent recommended vaccine formulations is described. Proteolytic digests of whole virus or separated hemagglutinin antigen generate conserved signature peptides of unique mass that can be used to characterise each component virus in a rapid and direct manner by the detection of their ions alone. The approach is demonstrated for two type A strains and one type B strain of human influenza viruses present in recommended seasonal vaccines in the northern and southern hemispheres from 2007 through 2010.