Glycoprotein analysis by delayed extraction and post-source decay MALDI-TOF-MS

Effective analysis of degree of polymerization of polysialic acids in mass spectrometry by combining novel sample preparation and dynamic instrument optimization methods

This work demonstrates a mass spectrometry technique to improve data reliability when analyzing degree of polymerization (DP) of high-mass polysialic acids (PSAs). Matrix-assisted laser-desorption/ionization (MALDI) time-of-flight mass spectrometry is the technique of choice for analyzing large molecules due to its wide mass working range; however, the observed DP of PSAs using such an instrument is unreliable owing to sensitivity bias towards low-mass ions. A multi-layer MALDI sample preparation protocol is demonstrated in the current study to improve PSA sensitivity, and a dynamic instrument optimization method (DIOM) is employed to minimize detector saturation over a wide mass range. The DP information obtained in the DIOM combines a series of mass spectral data obtained with individually optimized instrument parameters to minimize the problem of sensitivity bias in respective mass ranges. The resultant mass spectra facilitate unambiguous determination of DP in the high-mass range due to significantly improved spectral quality. The main instrument parameters involved in the optimization process include extraction delay in MALDI ion source as well as the cutoff mass of the ion detector. In comparison to conventional methods, the DIOM doubles the maximum DP that can be unambiguously identified by mass spectrometry.

Comprehensive Proteoform Characterization of Plasma Complement Component C8αβγ by Hybrid Mass Spectrometry Approaches

The human complement hetero-trimeric C8αβγ (C8) protein assembly (~ 150 kDa) is an important component of the membrane attack complex (MAC). C8 initiates membrane penetration and coordinates MAC pore formation. Here, we charted in detail the structural micro-heterogeneity within C8, purified from human plasma, combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The intact C8 proteoform profile revealed at least ~ 20 co-occurring MS signals. Additionally, we employed ion exchange chromatography to separate purified C8 into four distinct fractions. Their native MS analysis revealed even more detailed structural micro-heterogeneity on C8. Subsequent peptide-centric analysis, by proteolytic digestion of C8 and LC-MS/MS, provided site-specific quantitative profiles of different types of C8 glycosylation. Combining all this data provides a detailed specification of co-occurring C8 proteoforms, including experimental evidence on N-glycosylation, C-mannosylation, and O-glycosylation. In addition to the known N-glycosylation sites, two more N-glycosylation sites were detected on C8. Additionally, we elucidated the stoichiometry of all C-mannosylation sites in all the thrombospondin-like (TSP) domains of C8α and C8β. Lastly, our data contain the first experimental evidence of O-linked glycans located on C8γ. Albeit low abundant, these O-glycans are the first PTMs ever detected on this subunit. By placing the observed PTMs in structural models of free C8 and C8 embedded in the MAC, it may be speculated that some of the newly identified modifications may play a role in the MAC formation. Graphical Abstract ᅟ.

High resolution imaging and 3D analysis of Ag nanoparticles in cells with ToF-SIMS and delayed extraction

Within this study, the authors use human mesenchymal stem cells incubated with silver nanoparticles (AgNPs) as a model system to systematically investigate the advantages and drawbacks of the fast imaging delayed extraction mode for two-dimensional and three-dimensional (3D) analyses at the cellular level. The authors compare the delayed extraction mode with commonly employed measurement modes in terms of mass and lateral resolution, intensity, and dose density. Using the delayed extraction mode for single cell analysis, a high mass resolution up to 4000 at m/z = 184.08 combined with a lateral resolution up to 360 nm is achieved. Furthermore, the authors perform 3D analyses with Ar-clusters (10 keV) and O₂⁺ (500 eV) as sputter species, combined with Bi₃⁺ and delayed extraction for analysis. Cell compartments like the nucleus are visualized in 3D, whereas no realistic 3D reconstruction of intracellular AgNP is possible due to the different sputter rates of inorganic and organic cell materials. Furthermore, the authors show that the sputter yield of Ag increases with the decreasing Ar-cluster size, which might be an approach to converge the different sputter rates.

Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity

Many biopharmaceutical products exhibit extensive structural micro-heterogeneity due to an array of co-occurring post-translational modifications. These modifications often effect the functionality of the product and therefore need to be characterized in detail. Here, we present an integrative approach, combining two advanced mass spectrometry-based methods, high-resolution native mass spectrometry and middle-down proteomics, to analyse this micro-heterogeneity. Taking human erythropoietin and the human plasma properdin as model systems, we demonstrate that this strategy bridges the gap between peptide- and protein-based mass spectrometry platforms, providing the most complete profiling of glycoproteins. Integration of the two methods enabled the discovery of three undescribed C-glycosylation sites on properdin, and revealed in addition unexpected heterogeneity in occupancies of C-mannosylation. Furthermore, using various sources of erythropoietin we define and demonstrate the usage of a biosimilarity score to quantitatively assess structural similarity, which would also be beneficial for profiling other therapeutic proteins and even plasma protein biomarkers.

Many biopharmaceuticals exhibit mixed heterogeneity in their post-translational modifications (PTMs) that are essential for their function. Here the authors use a combination of mass spectrometry techniques to analyse human erythropoietin (EPO) and properdin to discover new PTMs on properdin and derive a biosimilarity score for various sources of EPO.

Critical factors determining the quantification capability of matrix-assisted laser desorption/ionization- time-of-flight mass spectrometry

Quantitative analysis with mass spectrometry (MS) is important but challenging. Matrix-assisted laser desorption/ionization (MALDI) coupled with time-of-flight (TOF) MS offers superior sensitivity, resolution and speed, but such techniques have numerous disadvantages that hinder quantitative analyses. This review summarizes essential obstacles to analyte quantification with MALDI-TOF MS, including the complex ionization mechanism of MALDI, sensitive characteristics of the applied electric fields and the mass-dependent detection efficiency of ion detectors. General quantitative ionization and desorption interpretations of ion production are described. Important instrument parameters and available methods of MALDI-TOF MS used for quantitative analysis are also reviewed.This article is part of the themed issue 'Quantitative mass spectrometry'.

Glycopeptide enrichment for MALDI-TOF mass spectrometry analysis by hydrophilic interaction liquid chromatography solid phase extraction (HILIC SPE)

Glycoproteins, and in particular glycopeptides, are highly hydrophilic and are often not retained by reversed phase (RP) chromatography. The separation principle of normal phase (NP) is based on hydrophilic interactions, which in many aspects is complementary to RP separations. Hydrophilic interaction liquid chromatography (HILIC) is a fairly new variation of the NP separations used in the 1970s, the major difference being the use of aqueous solvents. HILIC provides a versatile tool for enrichment of glycopeptides before mass spectrometric (MS) analysis, particularly when used for solid phase extraction (SPE), or in combination with other chromatographic resins or ion-pairing reagents. HILIC SPE can be used for glyco-profiling, i.e., for determining the glycan heterogeneity at one specific glycosylation site, for enrichment of glycopeptides from a complex mixture of peptides, as well as for pre-fractionation of complex samples at the protein or peptide level. In this chapter we present a straightforward HILIC SPE enrichment technique and then combine C18 RP and HILIC enrichment for analysis of glycopeptides. Finally, we demonstrate HILIC enrichment using trifluoroacetic acid as an ion-pairing reagent for the enrichment of glycopeptides prior to mass spectrometry analysis.

Global methods for protein glycosylation analysis by mass spectrometry

Mass spectrometry has been an analytical tool of choice for glycosylation analysis of individual proteins. Over the last 5 years several previously and newly developed mass spectrometry methods have been extended to global glycoprotein studies. In this review we discuss the importance of these global studies and the advances that have been made in enrichment analyses and fragmentation methods. We also briefly describe relevant sample preparation methods that have been used for the analysis of a single glycoprotein that could be extrapolated to global studies. Finally this review covers aspects of improvements and advances on the instrument front which are important to future global glycoproteomic studies.

Characterization ofN- andO-glycopeptides of recombinant human erythropoietins as potential biomarkers for doping analysis by means of microscale sample purification combined with MALDI-TOF and quadrupole IT/RTOF mass spectrometry

The structural characterization of the O- and N-glycan structures of three different commercially available recombinant human erythropoietins (rhEPOs) is represented by means of a microscale sample purification using ZipTip technology and MALDI-TOF and MALDI low-energy CID MS. Glycopeptides were released from rhEPO samples by a differential endoproteolytic digestion to obtain site-specific glycosylation patterns. Mass accuracies in the range of +/- 0.04% obtained by the high-resolution TOF instrument allowed an unambiguous assignment of N-glycan structures via glycan database software. Furthermore, the O-glycan structures were directly analyzed on the glycopeptide level by MS/MS experiments. Principally, site-specific glycosylation was found to be very similar for the three different rhEPOs (EPO-alpha, EPO-beta, and novel erythropoiesis stimulating protein (NESP)) but exhibiting quantitative differences in distinct O- and N-glycan moieties. Significant differences were found in the degree of sialylation and acetylation. Especially, a considerable degree of variation of the O-acetylation of sialic acid residues could be realized on the glycan structures of O- and N-glycopeptides, whereas EPO-alpha and EPO-beta could be clearly differentiated from NESP solely on the O-glycopeptide level.

Structural determination ofN-linked glycans by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry

This paper reviews methods for the analysis of N-linked glycans by mass spectrometry with emphasis on studies conducted at the Oxford Glycobiology Institute. Topics covered are the release of glycans from sodium dodecyl sulphate-polyacrylamide gel electrophoresis gels, their purification for analysis by mass spectrometry, methods based on matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization for producing fragment ions, and details of their fragmentation. MALDI mass spectrometry provided a rapid method for profiling neutral N-linked glycans as their [M + Na](+) ions which could be fragmented by collision-induced decomposition to give spectra containing both glycosidic and cross-ring fragments. Electrospray ionization mass spectrometry was more versatile in that it was relatively easy to change the type of ion that was formed and, furthermore, unlike MALDI, electrospray did not cause extensive loss of sialic acids from sialylated glycans. Negative ions formed by addition of anions such as chloride and, particularly, nitrate, to the electrospray solvent were stable and enabled singly charged ions to be obtained from larger glycans than was possible in positive ion mode. Fragmentation of negative ions followed specific pathways that defined structural details of the glycans that were difficult to obtain by classical methods such as exoglycosidase digestion.

Characterisation of intact recombinant human erythropoietins applied in doping by means of planar gel electrophoretic techniques and matrix-assisted laser desorption/ionisation linear time-of-flight mass spectrometry

Our experiments show that it is possible to detect different types of recombinant human erythropoietins (rhEPOs), EPO-alpha, EPO-beta and novel erythropoesis stimulating protein (NESP), based on exact molecular weight (MW) determination by matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) applying a high-resolution time-of-flight (TOF) mass analyser in the linear mode. Detection limits for the highly purified, intact glycoproteins were achievable in the low fmol range (25-50 fmol) using a sample preparation method applying a hydrophobic sample support (DropStop) as MALDI target surface. These results are very promising for the development of highly sensitive detection methods for a direct identification of rhEPO after enrichment from human body fluids. During our investigation we were able to differentiate EPO-alpha, EPO-beta and NESP based on distinct molecular substructures at the protein level by specific enzymatic reactions. MW determination of the intact molecules by high resolving one-dimensional sodium dodecyl sulfate /polyacrylamide gel electrophoresis (1D SDS-PAGE) and isoform separation by planar isoelectric focusing (IEF) was compared with MALDI-MS data. Migration differences between the rhEPOs were observed from gel electrophoresis, whereby MWs of 38 kDa in the case of EPO-alpha/beta and 49 kDa for NESP could be estimated. In contrast, an exact MW determination by MALDI-MS based on internal calibration revealed average MWs of 29.8 +/- 0.3 kDa for EPO-alpha/beta and 36.8 +/- 0.4 kDa for NESP. IEF separation of the intact rhEPOs revealed the presence of four to eight distinct isoforms in EPO-alpha and EPO-beta, while four isoforms, which appeared in the more acidic area of the gels, were detected by immunostaining in NESP. A direct detection of the different N- or O-glycoform pattern from rhEPOs using MALDI-MS was possible by de-sialylation of the glycan structures and after de-N-glycosylation of the intact molecules. Thereby, the main glycoforms of EPO-alpha, EPO-beta and NESP could be characterised based on their N-glycan composition. A microheterogeneity of the molecules based on the degree of sialylation of the O-glycan was observable directly from the de-N-glycosylated protein.

Matrix-assisted and polymer-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of low molecular weight polystyrenes and polyethylene glycols

Recently, matrices based on oligomers of dioxin and thiophene (polymer-assisted laser desorption/ionization (PALDI)) have been described for mass spectrometric (MS) analysis of low molecular weight compounds (Woldegiorgis A, von Kieseritzky F, Dahlstedt E, Hellberg J, Brinck T, Roeraade J. Rapid Commun. Mass Spectrom. 2004; 18: 841-852). In this paper, we report the use of PALDI matrices for low molecular weight polymers. An evaluation with polystyrene and polyethylene glycol showed that no charge transfer ionization occurs. Ionization is mediated through metal ion adduction. Comparison of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) data for two very low molecular weight polymers with data obtained from size-exclusion chromatography (SEC) revealed a systematic difference regarding mean molecular weight and dispersity. Further, the mass spectra obtained with PALDI matrices had a higher signal-to-noise ratio than the spectra obtained with conventional matrices. For polymers with higher molecular weights (>1500 Da), the conventional matrices gave better performance. For evaluation of the MALDI spectra, three non-linear mathematical models were evaluated to model the cumulative distributions of the different oligomers and their maximal values of Mw, Mn and PDI. Models based on sigmoidal or Boltzmann equations proved to be most suitable. Objective modeling tools are necessary to compare different sample and instrumental conditions during method optimization of MALDI analysis of polymers, since the bias between MALDI and SEC data can be misleading.

Mass spectrometry--a key technology in proteome research

The rapid developments in the field of mass spectrometry have transformed it into a key technology in proteome research. Increased sensitivity in mass spectrometry, as a result of more efficient ionisation techniques and better detectors, has allowed the stepwise reduction of protein quantity for analysis. Protein spots of 2D-PAGE separated samples are now quantitatively sufficient for an unequivocal identification of a protein by mass spectrometry. In addition to protein identification a closer look at posttranslational modifications is now also possible. It is speculated that modifications like phosphorylation or glycosylation exist on every second protein and that they are important for the protein function. This review highlights the different mass spectrometric methods and gives a brief overview of strategies and methods used to identify modifications.

A family of novel, acidic N-glycans in Bowes melanoma tissue plasminogen activator have L2/HNK-1-bearing antennae, many with sulfation of the fucosylated chitobiose core

A family of about 20 novel acidic bi- and tri-antennary N-glycans, amounting to almost half those expressed on Bowes melanoma tissue-plasminogen activator (t-PA) were found to possess Galbeta1-->4GlcNAcbeta1-->, sulfated and sialylated GalNAcbeta1-->4GlcNAcbeta1--> or sulfated GlcAbeta1--> 3Galbeta1-->4GlcNAcbeta1--> antennae, of which those containing sulfated GlcA, depicting the L2/HNK-1 carbohydrate epitope, were preferentially located on the 6 arm. A proportion of the glycans were highly charged, because of multiple and variously distributed sulfation, some of which was located on the fucosylated chitobiose core. Multiple expression of the L2/HNK-1 epitope on a single glycan was observed. The most abundant compound was a biantennary glycan carrying sulfated GlcA on the 6-branched antenna and an alpha2-->6 sialylated GalNAc on the other. The N-glycosylation sequon containing Asn448, which is known to express all of the sulfate-carrying N-glycans contains, unusually, an arginine residue. An electrostatic interaction between this cationic amino acid and the core-sulfate group of the N-glycan is proposed to reduce mobility of the carbohydrate in the region of the t-PA active site. Because of the 'brain-type' nature of the N-glycans described in this neuro-ectodermal cell line, the possibility of neural t-PA interacting with the L2/HNK-1-recognizing molecule, laminin, of the central nervous system extracellular matrix is discussed.

Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates

This review describes the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to carbohydrate analysis and covers the period 1991-1998. The technique is particularly valuable for carbohydrates because it enables underivatised, as well as derivatised compounds to be examined. The various MALDI matrices that have been used for carbohydrate analysis are described, and the use of derivatization for improving mass spectral detection limits is also discussed. Methods for sample preparation and for extracting carbohydrates from biological media prior to mass spectrometric analysis are compared with emphasis on highly sensitive mass spectrometric methods. Quantitative aspects of MALDI are covered with respect to the relationship between signal strength and both mass and compound structure. The value of mass measurements by MALDI to provide a carbohydrate composition is stressed, together with the ability of the technique to provide fragmentation spectra. The use of in-source and post-source decay and collision-induced fragmentation in this context is described with emphasis on ions that provide information on the linkage and branching patterns of carbohydrates. The use of MALDI mass spectrometry, linked with exoglycosidase sequencing, is described for N-linked glycans derived from glycoproteins, and methods for the analysis of O-linked glycans are also covered. The review ends with a description of various applications of the technique to carbohydrates found as constituents of glycoproteins, bacterial glycolipids, sphingolipids, and glycolipid anchors.

Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry

The potential of matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay (PSD) time-of-flight mass spectrometry for the characterization of peptides and proteins is discussed. Recent instrumental developments provide for levels of sensitivity and accuracy that make these techniques major analytical tools for proteome analysis. New software developments employing protein database searches have greatly enhanced the fields of application of MALDI-PSD. Peptides and proteins can be easily identified even if only a partial sequence information is determined. Derivatization procedures have been optimized for MALDI-PSD to increase the structural information and to obtain a complete peptide sequence even in critical cases. They are fast, simple and can be performed on target. MALDI-PSD is also a very powerful tool to characterize or elucidate post-translational or chemically induced modifications. In association with database searches, proteins issued from electrophoretic gels can be identified after specific enzymatic cleavages and peptide mapping.

Effect of 1-phenyl-3-methyl-5-pyrazolone labeling on the fragmentation behavior of asialo and sialylated N-linked glycans under electrospray ionization conditions

The advantages of labeling free N-linked oligosaccharides with 1-phenyl-3-methyl-5-pyrazolone (PMP), for high performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS) are discussed. The study focuses on some asialo and sialylated sugars, and compares the HPLC and ESI-MS behaviors of the PMP-labeled substances vs. the native compounds. It is pointed out that native free N-linked carbohydrates have very low affinities for the C18 reversed phases commonly used in HPLC. Native asialo oligosaccharides yield good ESI-MS sensitivity, although they are very susceptible to in-source collision-induced dissociation (CID), and the fragments are produced from any of the branches of the molecules, i.e. do not give specific structural information. Native N-linked standards bearing one sialic acid residue yield a 10-fold loss of ESI-MS sensitivity vs. asialo compounds, and native sugars with two sialic acid moieties were not detectable. The PMP labeling of asialo and sialylated sugars yielded higher affinities for HPLC C18 columns and, even at the early stages of method development, it was possible to separate three PMP-labeled standards to a useful extent. In ESI-MS, PMP-asialo sugars did not yield a significant increase in sensitivity vs. the native species; however, fragmentation produced by in-source CID was more directed as all predominant fragment ions contained the bis-PMP label. This feature is particularly useful when structural determination of an unknown sugar is required. PMP-sialylated sugars gave rise to very clean and informative ESI mass spectra. The monosialo sugar yielded a 100-fold sensitivity improvement vs. its native analog and, in the case of the disialylated compound, a 100% improvement was obtained in the positive mode. Most fragment ions were informative and contained the reducing end on the molecules, thus facilitating spectral interpretation. The combination of PMP derivatization with on-line HPLC/ESI-MS is a promising method for the analysis of asialo and sialylated carbohydrate mixtures.