Stephan Warnke

École Polytechnique Fédérale de Lausanne | EPFL · SB ISIC LCPM

The structural complexity of glycans makes their characterization challenging, not only because of the presence of various isomeric forms of the precursor molecule but also because the fragments can themselves be isomeric. We have recently developed an IMS-CID-IMS approach using structures for lossless ion manipulations (SLIM) combined with cryogen...

Glycan analysis has evolved considerably during the last decade. The advent of high-resolution ion-mobility spectrometry has enabled the separation of isomers with only the slightest of structural differences. However, the ability to separate such species raises the problem of identifying all the mobility-resolved peaks that are observed, especiall...

Determining the primary structure of glycans remains challenging due to their isomeric complexity. While high-resolution ion mobility spectrometry (IMS) has recently allowed distinguishing between many glycan isomers, the arrival-time distributions (ATDs) frequently exhibit multiple peaks, which can arise from positional isomers, reducing-end anome...

Coupling vibrational ion spectroscopy with high-resolution ion mobility separation offers a promising approach for detailed analysis of biomolecules in the gas phase. Improvements in the ion mobility technology have made it possible to separate isomers with minor structural differences, and their interrogation with a tunable infrared laser provides...

While glycans are present on the surface of cells in all living organisms and play key roles in most biological processes, their isomeric complexity makes their structural characterization challenging. Of particular importance are positional isomers, for which analytical standards are difficult to obtain. We combine ultrahigh-resolution ion-mobilit...

The analysis of glycans presents a significant challenge that arises from their isomeric heterogeneity. While high-resolution ion mobility spectrometry (IMS) has shown the ability to resolve subtly different glycan isomers, their unambiguous assignment remains difficult. Here, we demonstrate an infrared (IR) spectroscopic approach for identifying i...

Infrared (IR) spectroscopy is a powerful tool used to infer detailed structural information on molecules, often in conjunction with quantum-chemical calculations. When applied to cryogenically cooled ions, IR spectra provide unique fingerprints that can be used for biomolecular identification. This is particularly important in the analysis of isome...

Glycosylation patterns in monoclonal antibodies (mAbs) can vary significantly between different host cell types, and these differences may affect mAbs safety, efficacy, and immunogenicity. Recent studies have demonstrated that glycan isomers with the terminal galactose position on either the Man α1-3 arm or the Man α1-6 arm have an impact on the ef...

The isomeric heterogeneity of glycans poses a great challenge for their analysis. While combining ion mobility spectrometry (IMS) with tandem mass spectrometry is a powerful means for identifying and characterizing glycans, it has difficulty distinguishing the subtlest differences between isomers. Cryogenic infrared spectroscopy provides an additio...

While mass spectrometry alone lacks the ability to resolve glycan isomers, combining it with cryogenic ion spectroscopy and ion mobility spectrometry (IMS) has been recently shown to be extremely sensitive to glycan structure. However, these methods are only partially suitable for larger glycans. Many glycans present a large number of isomeric stru...

Despite the essential role that glycans play in many biological processes, their isomeric complexity makes their structural determination particularly challenging. Tandem mass spectrometry has played a central role in glycan analysis, and recent work has shown that fragments generated by collision-induced dissociation (CID) of disaccharides can ret...

Mass spectrometry enables the in-depth structural elucidation of membrane protein complexes, which is of great interest in structural biology and drug discovery. Recent breakthroughs in this field revealed the need for design rules that allow fine-tuning the properties of detergents in solution and gas phase. Desirable features include protein char...

The analysis of carbohydrates, or glycans, is challenging for established structure-sensitive gas-phase methods. The multitude of possible stereo-, regio-, and structural isomers makes them substantially more complex to analyze than DNA or proteins, and no one method is currently able to fully resolve them. While the combination of tandem mass spec...

The analysis of carbohydrates, or glycans, is challenging for established structure-sensitive gas-phase methods. The multitude of possible stereo-, regio-, and structural isomers makes them substantially more complex to analyze than DNA or proteins, and no one method is currently able to fully resolve them. While the combination of tandem mass spec...

The isomeric complexity of glycans make their analysis by traditional techniques particularly challenging. While the recent combination of ion mobility spectrometry (IMS) with cryogenic IR spectroscopy has demonstrated great promise as a new technique for glycan analysis, this approach has been limited by the modest resolution of the ion mobility s...

The amino acid serine is long known to form a protonated “magic-number” cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser8H⁺ structure that is in agreement with all experimental ob...

Double-resonance spectroscopic schemes in combination with cryogenic ion traps are the go-to techniques when isomer-specific high-resolution spectra are required for analysis of molecular ions. Their limitation lies in the requirement for well-resolved, isomer-specific absorption bands as well as in the potentially time-consuming steps to identify...

The amino acid serine is known to form a very stable octamer that has properties that set it apart from serine complexes of different sizes or from complexes composed of other amino acids. For example, both singly protonated serine octamers and anionic octamers complexed with two halogen ions strongly prefer homochirality, even when assembled from...

A protonated amino acid can interact in several ways with another uncharged amino acid molecule to form a protonated dimer. In case of amino acids that do not have basic or acidic side chains, the most likely protonation site is the amino group and the then protonated amine can be involved in a pairwise interaction with a neutral amine, a carboxyli...

In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures...

Amphiphilic porphyrins are of great interest in the field of supramolecular chemistry because they can be fabricated into highly-ordered architectures that are stabilized by π-π stacking of porphine rings as well as by non-covalent interactions between their hydrophilic substituents. Protoporphyrin IX (PPIX) has two flexible propionic acid tails an...

Supplementary

In this study the gas-phase structure of ubiquitin and its lysine-to-arginine mutants was investigated using ion mobility-mass spectrometry (IM-MS) and electron transfer dissociation-mass spectrometry (ETD-MS). Crown ether molecules were attached to positively charged sites of the proteins and the resulting non-covalent complexes were analyzed. Col...

In this study the gas-phase structure of ubiquitin and its lysine-to-arginine mutants was investigated using ion mobility-mass spectrometry (IM-MS) and electron transfer dissociation-mass spectrometry (ETD-MS). Crown ether molecules were attached to positive charge sites of the proteins and the resulting non-covalent complexes were analysed. Collis...

Amyloidogenic peptides and proteins play a crucial role in a variety of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. These proteins undergo a spontaneous transition from a soluble, often partially folded form, into insoluble amyloid fibrils that are rich in β-sheets. Increasing evidence suggests that highly dynamic, poly...

Electrospray ionization is routinely used to release proteins into the gas phase, but it is still not clear how much of the native structure can be retained. In their Communication (DOI: 10.1002/anie.201606029), G. von Helden and co-workers present the results of a combination of ion-mobility mass spectrometry and IR spectroscopy techniques, which...

Elektrosprayionisation wird routinemäßig eingesetzt, um Proteine in die Gasphase zu bringen, doch es ist noch nicht klar, wie viel von der nativen Proteinstruktur bei diesem Prozess erhalten bleibt. In ihrer Zuschrift (DOI: 10.1002/ange.201606029) berichten G. von Helden et al. über eine Kombination von Ionenmobilitäts-Massenspektrometrie mit IR-Sp...

Can the structures of small to medium-sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrome...

The charge distribution in a molecule is crucially determining its physical and chemical properties. Aminobenzoic acid derivatives are biologically active small molecules, which have two possible protonation sites: the amine (N-protonation) and the carbonyl oxygen (O-protonation). Here, we employ gas-phase infrared spectroscopy in combination with...

So-called super-secondary structures such as the β-hairpin, studied here, form an intermediate hierarchy between secondary and tertiary structures of proteins. Their sequence-derived ‘pure’ peptide backbone conformation is combined with ‘remote’ interstrand or interresidue contacts reminiscent of the 3D-structure of full-length proteins. This rende...

Kann die Struktur kleinerer bis mittelgroßer Proteine beim Übergang aus der Lösung in die Gasphase bewahrt werden? Zwar haben sich eine Vielzahl von Studien dieser Frage gewidmet, jedoch steht eine eindeutige Antwort noch aus. Die Klärung dieses Problems ist gleichwohl wichtig, denn davon hängt es ab, ob die empfindlichen Methoden der nativen Masse...

Polyalanine based peptides that carry a lysine at the C-terminus ([Ac-AlanLys + H]+) are known to form [small alpha]-helices in the gas phase. Three factors contribute to the stability of these helices: I) the interaction between the helix macro dipole and the charge, II) the capping of dangling C=O groups by lysine and III) the cooperative hydroge...

The solution-phase photooxygenation of multiply threaded crown/ammonium pseudorotaxanes containing anthracene spacers is monitored by electrospray ionization Fourier-transform ion-cyclotron-resonance (ESI-FTICR) mass spectrometry. The oxygenated pseudorotaxanes are mass-selected and fragmented by infrared multiphoton dissociation (IRMPD) and/or col...

IR spectroscopy of protonated benzocaine

Ion mobility-mass spectrometry was used to obtain detailed information about the kinetics of the light-induced trans/cis isomerization process of a new supramolecular azobenzene-based bolaamphiphile. Further experiments revealed that the investigated light-induced structural transition dramatically influences the aggregation behaviour of the molecu...

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid, which finds an application as a local anesthetic (LA), is found to adopt in its protonated form at least two populations of distinct structures in the gas phase and their relative intensities strongly depen...

A reliable, quantitative prediction of the structure of peptides based on their amino-acid sequence information is an ongoing challenge. We here explore the energy landscape of two unsolvated 20-residue peptides that result from a shift of the position of one amino acid in otherwise the same sequence. Our main goal is to assess the performance of c...

The top-down approach in protein sequencing requires simple methods in which the analyte can be readily dissociated at every position along the backbone. In this context, ultraviolet photodissociation (UVPD) recently emerged as a promising tool because, in contrast to slow heating techniques such as collision induced dissociation (CID), the absorpt...

In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted [small beta] amino acids. We specifically designed the [small beta] peptide Ac-([small beta]2hAla)6-LysH+...

Ultraviolet photodissociation (UVPD) of gas-phase proteins has attracted increased attention in recent years. This growing interest is largely based on the fact that, in contrast to slow heating techniques such as collision induced dissociation (CID), the cleavage propensity after absorption of UV light is distributed over the entire protein sequen...

Specific interactions between cations and proteins have a strong impact on peptide and protein structure. Herein, we shed light on the nature of the underlying interactions, especially regarding effects on the polyamide backbone structure. This was done by comparing the conformational ensembles of model peptides in isolation and in the presence of...

There is ongoing debate on the extent to which protein structure is retained after transfer into the gas phase. Here using ion mobility mass spectrometry, we investigate the impact of side-chain backbone interactions on the structure of gas-phase protein ions by non-covalent attachment of crown ethers (CE). Our results indicate that in the absence...

In the transition from secondary to tertiary structure in peptides and proteins, turns take a special role. They are the hinges that arrange the periodic secondary structure elements (helices and strands) to the native fold. It is a known effect that Li+ alters peptide backbone structure,[1] and we investigate this effect on the structure and dynam...