Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology.

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has unique capabilities in the area of high-resolution mass spectrometric imaging of biological samples. The technique offers parallel detection of native and non-native molecules at physiological concentrations with potentially submicrometer spatial resolution. Recent advances in SIMS technology have been focused on generating new ion sources that can in turn be used to eject more intact molecular and biological characteristic species from a sample. The introduction of polyatomic ion beams, particularly C60, for TOF-SIMS analysis has created a whole new application of molecular depth profiling and 3D molecular imaging. However, such analyses, particularly at high lateral resolution, are severely hampered by the accompanying mass spectrometry associated with current TOF-SIMS instruments. Hence, we have developed an instrument that overcomes many of the drawbacks of current TOF-SIMS spectrometers by removing the need to pulse the primary ion beam. T...

A new dynamic in mass spectral imaging of single biological cells.

Characterisation of various grape seed oils by volatile compounds, triacylglycerol composition, total phenols and antioxidant capacity.

The possibility of exploiting the analytical power of mass spectrometry to image the chemistry of biological and similarly complex materials without the use of tags and with good spatial resolution is seductive. The status, strengths, weaknesses and complementarity of the three main techniques are briefly reviewed and assessed.

Molecular imaging and depth profiling by mass spectrometry--SIMS, MALDI or DESI?

This review describes the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates and continues coverage of the field from the previous review published in 1999 (D J Harvey, Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates, 1999, Mass Spectrom Rev, 18:349-451) for the period 1999-2000 As MALDI mass spectrometry is acquiring the status of a mature technique in this field, there has been a greater emphasis on applications rather than to method development as opposed to the previous review The present review covers applications to plant-derived carbohydrates, N- and O-linked glycans from glycoproteins, glycated proteins, mucins, glycosaminoglycans, bacterial glycolipids, glycosphingolipids, glycoglycerolipids and related compounds, and glycosides Applications of MALDI mass spectrometry to the study of enzymes acting on carbohydrates (glycosyltransferases and glycosidases) and to the synthesis of carbohydrates, are also covered

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update covering the period 1999–2000

Immediately after the first MALDI-TOF instrument became available, microbiologists have been investigating its potential as a platform for high throughput identification of microorganisms. A remarkable finding very early in these investigations was that despite the dynamic nature of the bacterial cell, components of the mass spectral profile were sufficiently stable and remained unchanged in spite of changes in environmental parameters. Further, mass spectral patterns have been found to be taxon specific, consequently, numerous methods were reported that purported to provide an alternative to current identification systems. The SARAMIS system described herein sequentially extracts core stable mass ions from analyses of multiple individual strains of a particular species to yield a ‘SuperSpectrum’, a list of biomarkers that are weighted according to their specificity from family to (sub)species levels. This approach has been used successfully to identify microorganisms from diverse phylogenetic lines of bacteria and fungi with considerable success. The protocol described has evolved of over years of experimental work to yield a robust system that can be readily applied for microbiological identification in a clinical diagnostic laboratory. Identification of Microorganisms in Clinical Routine A crucial step in the epidemiology and the successful therapy of any infectious disease is the identification of the causative microbe. For more than a century, clinical microbiology has relied on the isolation of the suspected pathogen from various samples such as stools, throat swabs, blood, or urine on selective growth media and an identification procedure that is based on the metabolic capacities of the isolate. An array of carbohydrate fermentation and enzymatic reactions are tested that generally involve a colour change of an indicator when a particular substrate is catabolised. The profile of positive and negative reactions is assumed to be characteristic for a bacterial taxon and is consequently used for identification. Modern microbial identification systems are miniaturized, combining some tens of reactions into a single strip or card to allow for high throughput analysis. The major shortcomings of these systems are the need to incubate isolates for several hours to obtain pure cultures, and a required pre-selection of tests. Although this is still the most commonly used method in clinical diagnostic laboratories, microbiologists have been seeking alternative methods for the identification of pathogens for decades. A new era has dawned with the arrival of molecular methods such as the polymerase chain reaction (PCR) and nucleotide sequence analysis. In diagnostic and systematic microbiology today, analysis of genomic sequences is rapidly displacing biochemical tests for the provision of new characters for the circumscription of taxa. For example, a prerequisite for the description of a new species is the inclusion of the sequence of the 16S rRNA gene which now plays a pivotal role in microbial phylogeny. However, despite the widespread use of PCR and sequencing in all fields of microbiology, the technology is still lagging behind in clinical microbiology and is Shah, Gharbia, Encheva (Eds.) Mass spectrometry for microbial proteomics largely restricted to research applications. On the other hand, the high sensitivity and specificity of molecular methods make them indispensable in modern microbiological laboratories, as for example in the detection of methicillin resistant Staphylococcus aureus (MRSA) by real-time PCR assays, or the identification of atypical or very rare pathogens. Mass Spectrometry and Microbiology The application of chemical analyses (referred to as chemotaxonomy) for the identification and classification of microorganisms has been explored extensively prior to molecular analysis. These were based on the characterisation of polar (eg. phospholipids) and non polar lipids such as respiratory quinones (eg. ubiquinones and menaquinones) and long-chained cellular fatty acids . The structure of these lipids were challenging and ushered in a period of intense mass spectral analysis to characterise the vast array of lipids present in the microbial kingdom. While these methods provided characters at the genus and species levels, pyrrolysis mass spectrometry was introduced as a means of typing bacterial isolates . Such approaches were motivated by the need for a rapid method to identify pathogens in only a fraction of the time required for biochemical tests. However, because of the limitations of the technology at that time, mass spectral approaches were confined to the detection of organic molecules in a mass range up to 1,500 Da . Detection of larger molecules was hitherto only possible with techniques such as plasma desorption mass spectrometry . But this was about to change dramatically within a few years with the invention of Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and its success in many fields of life sciences has been phenomenal. The laser desorption and mass spectral analysis of large biomolecules was developed simultaneously by two research groups in Japan and Germany. While the group of Tanaka could successfully detect proteins up to m/z 100,000 Da by direct laser ionization , Karas and Hillenkamp 6 relied on a light absorbing matrix, and achieved similar results by this method. A matrix effect on the desorption rate was observed earlier for smaller molecules 7 and further studies quickly directed the search for matrix candidates to a few small organic molecules that are still the primarily used ones in MALDI-TOF MS applications today, viz. cinnamic acid derivatives 8 and 2,5dihydro benzoic acid . Accuracy and resolution could be significantly improved by the introduction of delayed ion extraction , which compensates for the variability in initial ion velocity . The sensitivity of MALDI-TOF MS for the detection of large proteins was rapidly increased to the femtomolar range 12 and further, aided by sophisticated handling procedures to the zeptomolar range . Within less then a decade, MALDI-TOF MS developed into a widely applied methodology in diverse fields of life sciences , promoted by a number of major advantages it had compared to other mass spectral technologies. These included the possibility to detect unfragmented large molecules, the speed with which a full scan over a wide mass range can be achieved, and the simplicity of sample preparation. For the analysis of whole cells and crude extracts, an outstanding advantage of MALDI compared to other ionization techniques such as electrospray ionization (ESI) or fast atom bombardment (FAB), is the fact that in MALDITOF MS predominantly singly charged ions are detected 15 which simplified the interpretation and treatment of mass spectral data considerably . Mass Spectral ‘Fingerprints’ of Whole Cells The possibility of introducing whole cells into a mass spectrometer and detecting biomolecules in a mass range extending to several kilodaltons was immediately recognised by microbiologists. Shortly after the first MALDI-TOF MS was commercially available (by Vestec and Kratos) the first reports on intact cell mass spectrometry of bacteria were published, some of which highlighted its potential for microbial diagnostics . Essentially these studies showed that mass spectra of whole cells of bacterial strains revealed patterns of mass signals that were reproducible and specific for strains or species. Because cells could be analysed after minimal processing and preparation, required only minute biomass, either as a cell suspension or cells placed directly on a target plate, the implications for diagnostic microbiology were immediately evident and numerous studies ensued. The mass ranges that were selected in early studies varied from m/z 500-2200 18 to m/z 200020000 . In the lower mass range, constituents of the cell wall are detected, and also, but to a lesser degree protein components . The lower mass range was also used for the typing of potentially toxic cyanobacteria 24 and proved to be suitable for the metabolic typing of sub-specific taxonomic units in natural populations . The possibility that mass fingerprints could be used to classify and eventually identify Kallow et al: MALDI-TOF MS for Microbial Identification 3 unknown microbial isolates was pursued in the following years by a number of groups. Most studies focused on the detection of proteins in mass ranges spanning from above m/z 2000 to below m/z 25,000. The identity of proteins detected at this time was not very clear because only a few genomic sequences of microorganisms were available. It was generally assumed that the proteins desorbed from whole cells, that were not subjected to typical mechanical or chemical lysis, were attached to the cell surface . However, studies on membrane-associated proteins of E. coli K12, revealed that the molecular mass of most of these proteins exceeded 20 kDa 26 and were likely to be intracellular proteins. Comparative MALDI-TOF mass spectral studies of isolated ribosomal subunits with those of whole cell mass spectra of E. coli K12 revealed that they shared a large number of mass signals that are commensurate with ribosomal proteins 27 (Figure 1). This large number of ionised ribosomal proteins is in accord with the high level of these proteins (ca. 30% of total proteins) of a cell in its exponential growth phase. Furthermore, studies on isolated ribosomes also revealed that many proteins were modified posttranslationally, and that the observed mass signals were in agreement with the general rules for methionine cleavage . Such studies emphasised that direct ‘translation’ of genomic data in mass patterns is not straightforward. Further microbial taxa have been studied in detail to reveal the identity of proteins detected by whole cell mass spectrometry. A high level of observed peaks in mass spect

MALDI-TOF MS for Microbial Identification: Years of Experimental Development to an Established Protocol

A commercial matrix-assisted laser desorption/ionisation time-of-flight (MALDI-ToF) instrument equipped with a curved field reflectron (CFR) was modified in order to perform collision-induced dissociation (CID) on a variety of biomolecules. The incorporation of a high-resolution ion gate together with a collision cell within the field-free region allowed tandem mass analysis (MS/MS), without the necessity to decelerate the precursor ions prior to activation. The simultaneous detection of all product ions remained possible by using the CFR. To test the MS/MS performances, ACTH (fragment 1-17), a complex high mannose carbohydrate (Man)(8)(GlcNac)(2) and a lysophosphatidylcholine lipid (18:1) were analysed on the modified instrument. Direct comparison with the low-energy product ion spectra, acquired on a MALDI quadrupole ion trap (QIT) two-stage reflectron time-of flight (ReToF) mass spectrometer, showed significant differences in the types of product ions observed. The additional ions detected were a clear indication of the high-energy fragmentation processes occurring in the collision cell.

Dissociation of biomolecules using a ultraviolet matrix-assisted laser desorption/ionisation time-of-flight/curved field reflectron tandem mass spectrometer equipped with a differential-pumped collision cell

A tandem time-of-flight (TOF-TOF) mass spectrometer comprised of two ion mirrors is described. The first ion mirror, which is a linear-field, single-stage mirror (MS1) with an intermediate collision cell, has been designed to provide the temporal focus necessary for the second, quadratic-field ion mirror (MS2) to function effectively. Due to the wide energy-range focusing capabilities of the quadratic field employed in the second ion mirror all the fragment ions can be collected in one spectrum without the need to step the reflecting working voltage of the MS2. The size of the active area of the microchannel plate detector used in the preliminary experiments was the limiting factor governing the collection efficiently of fragment ions. The use of the first ion mirror to provide temporal focusing of the precursor ion packet at the first focal point of the quadratic mirror used as the MS2 requires no alteration of the focusing conditions for different masses, in contrast to delayed extraction or postsource pulsed focusing. Precursor ions formed by matrix-assisted laser desorption/ionization were mass-selected with an ion gate located before the collision cell and the fragment ions were mass analyzed using the quadratic-field ion mirror. Experimental results demonstrating effective high-energy collision-induced dissociation of polymer and fullerene molecule-ions are presented.

Tandem time-of-flight mass spectrometer (TOF-TOF) with a quadratic-field ion mirror

Pitfalls on the road to the ideal time-of-flight mirror: ideal time-focusing in the second stage of tandem mass spectrometers

A tandem mass spectrometer consisting of a double-focusing magnetic-sector mass analyzer in series with a time-of-flight (TOF) mass analyzer has been designed and constructed. The TOF analyzer was a quadratic-field ion mirror. The method of ionization used was matrix-assisted laser desorption/ionization. Precursor ions were mass selected with the magnetic-sector analyzer, and time focused by ion bunching prior to fragmentation in a collision cell. The fragment ions were mass analyzed with the TOF analyzer, which possessed the property that residence times (i.e., times of flight) in the mirror were independent of ion velocity. The theoretical background to the instrumental design is presented. Experimental results are presented, showing resolutions of 4000 in fragment ion spectra and demonstrating effective high-energy collision-induced decomposition of peptide molecule ions.

Emmanuel Raptakis

Papers

MALDI-TOF MS for Microbial Identification: Years of Experimental Development to an Established Protocol

Dissociation of biomolecules using a ultraviolet matrix-assisted laser desorption/ionisation time-of-flight/curved field reflectron tandem mass spectrometer equipped with a differential-pumped collision cell

Tandem time-of-flight mass spectrometer (TOF-TOF) with a quadratic-field ion mirror

Pitfalls on the road to the ideal time-of-flight mirror: ideal time-focusing in the second stage of tandem mass spectrometers

In-series combination of a magnetic-sector mass spectrometer with a time-of-flight quadratic-field ion mirror