Fundamentals and applications of Maldi-Tof MS

MALDI was developed for the ionisation of relatively large polypeptides and proteins but its application has widened to incorporate glycoproteins, oligonucleotides and complex carbohydrates. A great advantage of MALDI TOF MS is that the process of soft-ionisation causes little or no fragmentation of analytes, allowing the molecular ions of analytes to be identified, even within mixtures. MALDI TOF MS analysis is sensitive and very rapid as once the sample has been mixed with a 'matrix' on a MALDI target, a spectrum can be generated within seconds. Hence, the majority of protein and oligonucleotide analysis in the context of high throughput proteomics and genomics is carried out by MALDI TOF mass spectrometry.

Further characterization of the subunits of the giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) by SDS-PAGE electrophoresis and MALDI-TOF-MS

Further characterization of hemoglobin of Glossoscolex paulistus (HbGp) subunits was performed based on SDS-PAGE, size exclusion chromatography (SEC) and MALDI-TOF-MS analysis. SDS-PAGE has shown a total of four linker chains, two quite intense and two of lower intensity. HbGp fractions (I-VI), obtained by size exclusion chromatography (SEC), from oligomeric dissociation at alkaline pH 9.6, were monitored. Fraction I is identical to the whole protein. The monomeric chains c, obtained from the trimer abc reduction, present four isoforms with MM 17,336 Da, 17,414 Da, 17,546 Da and 17,620 Da. Furthermore, the trimer subunit presents two isoforms, T 1 and T 2, with MM 51,200 ± 60 and 51,985 ± 50 Da, respectively. Based on SDS-PAGE, the linker chains seem to be distributed along the different fractions of the SEC chromatogram, appearing along the peaks corresponding to fractions I-V. The fraction IV contains, predominantly, trimers with some linkers contamination. The strong interaction of linker chains L with the trimers abc, makes it difficult to obtain these subunits in pure form. The monomer d in fraction VI appears to be quite pure, in agreement with previous studies. © 2011 Elsevier Ltd. All rights reserved.

Interaction of giant extracellular Glossoscolex paulistus hemoglobin (HbGp) with ionic surfactants: A MALDI-TOF-MS study

The giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) is constituted by approximately 144 subunits containing heme groups with molecular masses in the range of 16-19 kDa forming a monomer (d) and a trimer (abc), and around 36 non-heme structures, named linkers (L). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF-MS) analysis was performed recently, to obtain directly information on the molecular masses of the different subunits from HbGp in the oxy-form. This technique demonstrated structural similarity between HbGp and the widely studied hemoglobin of Lumbricus terrestris (HbLt). Indeed, two major isoforms (d(1) and d(2)) of identical proportions with masses of 16,355+/-25 and 16,428+/-24 Da, respectively, and two minor isoforms (d(3) and d(4)) with masses around 16.6 kDa were detected for monomer d of HbGp. In the present work, the effects of anionic sodium dodecyl sulfate (SDS) and cationic cethyltrimethyl ammonium chloride (CTAC) on the oligomeric structure of HbGp have been studied by MALDI-TOF-MS in order to evaluate the interaction between ionic surfactants and HbGp. The data obtained with this technique show an effective interaction of cationic surfactant CTAC with the two isoforms of monomer d, d(1) and d(2), both in the whole protein as well as in the pure isolated monomer. The results show that up to 10 molecules of CTAC are bound to each isoform of the monomer. Differently, the mass spectra obtained for SDS-HbGp system showed that the addition of the anionic surfactant SDS does not originate any mass increment of the monomeric subunits, indicating that SDS-HbGp interaction is, probably, significantly less effective as compared to CTAC-HbGp one. The acid pI of the protein around 5.5 is, probably, responsible for this behavior. The results of this work suggest also some interaction of both surfactants with linker chains as well as with trimers, as judged from observed mass increments. Our data are consistent with a recent spectroscopic study showing a strong interaction between CTAC and HbGp at physiological pH [P.S.Santiago, et al, Biochim. Biophys. Acta. 1770 (2007) 506-517.]. (C) 2007 Elsevier B.V. All rights reserved.

Cooking Effects on Iron and Proteins Content of Beans (Phaseolus Vulgaris L.) by GF AAS and MALDI-TOF MS

The effects of domestic cooking on proteins, organic compounds and Fe distribution in beans (Phaseolus vulgaris L.) were investigated. Sequential extraction with different extractant solutions (mixture of methanol and chloroform 1:2 v/v, water, 0.5 mol L-1 NaCl, 70% v/v ethanol and 0.5 mol L-1 NaOH) were used for extracting lipids, albumins, globulins, prolamins and glutelins, respectively. Iron determination by graphite furnace atomic absorption spectrometry (GF AAS), proteins by Bradford method and organic compounds by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were carried out in this work. High concentration of albumins, globulins and glutelins were found in raw beans, while in the cooked beans, albumins and glutelins are main proteins types. The MALDI-TOF MS spectra of raw and cooked beans revealed that the domestic cooking altered the molecular weight of the organic compounds, since that in the cooked beans were found compounds between 2 and 3.5 kDa, which were not presented in the raw beans. Besides this, in cooked beans were also observed the presence of four compounds of high molecular weight (12-16 kDa), being that in the raw grains there is only one (ca. 15.2 kDa). In raw grains is possible to observe that Fe is mainly associated to albumins, globulins and glutelins. For cooked grains, Fe is associated to albumins and globulins.

Cooking effects on iron and proteins content of beans (Phaseolus Vulgaris L.) by GF AAS and MALDI-TOF MS

The effects of domestic cooking on proteins, organic compounds and Fe distribution in beans (Phaseolus vulgaris L.) were investigated. Sequential extraction with different extractant solutions (mixture of methanol and chloroform 1:2 v/v, water, 0.5 mol L-1 NaCl, 70% v/v ethanol and 0.5 mol L-1 NaOH) were used for extracting lipids, albumins, globulins, prolamins and glutelins, respectively. Iron determination by graphite furnace atomic absorption spectrometry (GF AAS), proteins by Bradford method and organic compounds by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were carried out in this work. High concentration of albumins, globulins and glutelins were found in raw beans, while in the cooked beans, albumins and glutelins are main proteins types. The MALDI-TOF MS spectra of raw and cooked beans revealed that the domestic cooking altered the molecular weight of the organic compounds, since that in the cooked beans were found compounds between 2 and 3.5 kDa, which were not presented in the raw beans. Besides this, in cooked beans were also observed the presence of four compounds of high molecular weight (12-16 kDa), being that in the raw grains there is only one (ca. 15.2 kDa). In raw grains is possible to observe that Fe is mainly associated to albumins, globulins and glutelins. For cooked grains, Fe is associated to albumins and globulins.

Uso de espectrometria de massa por ionização e dessorção a laser assistida por matriz : tempo de voo (MALDI-TOF MS) para formação de bibliotecas e caracterização da ocupação nodular em soja por estirpes de Bradyrhizobium

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Biologia Microbiana, 2016.

Assessment of MALDI-TOF MS as Alternative Tool for Streptococcus suis Identification

The accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identifying Streptococcus suis isolates obtained from pigs, wild animals, and humans was evaluated using a PCR-based identification assay as the gold standard. In addition, MALDI-TOF MS was compared with the commercial multi-tests Rapid ID 32 STREP system. From the 129 S. suis isolates included in the study and identified by the molecular method, only 31 isolates (24.03%) had score values ≥2.300 and 79 isolates (61.24%) gave score values between 2.299 and 2.000. After updating the currently available S. suis MALDI Biotyper database with the spectra of three additional clinical isolates of serotypes 2, 7, and 9, most isolates had statistically significant higher score values (mean score: 2.65) than those obtained using the original database (mean score: 2.182). Considering the results of the present study, we suggest using a less restrictive threshold score of ≥2.000 for reliable species identification of S. suis. According to this cut-off value, a total of 125 S. suis isolates (96.9%) were correctly identified using the updated database. These data indicate an excellent performance of MALDI-TOF MS for the identification of S. suis.

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Amazonian Vegetable Oils and Fats: Fast Typification and Quality Control via Triacylglycerol (TAG) Profiles from Dry Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry Fingerprinting

Amazonian oils and fats display unique triacylglycerol (TAG) profiles and, because of their economic importance as renewable raw materials and use by the cosmetic and food industries, are often subject to adulteration and forgery. Representative samples of these oils (andiroba, Brazil nut, buriti, and passion fruit) and fats (cupuacu, murumuru, and ucuba) were characterized without pre-separation or derivatization via dry (solvent-free) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Characteristic profiles of TAG were obtained for each oil and tat. Dry MALDI-TOF MS provides typification and direct and detailed information, via TAG profiles, of their variable combinations of fatty acids. A database from spectra could be developed and may be used for their fast and reliable typification, application screening, and quality control.

Isolation and sequence determination of peptides in the venom of the spider wasp (Cyphononyx dorsalis) guided by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry

Micro-scale (sub-pmol) isolation and sequence determination of three peptides from the venom of the solitary spider wasp Cyphononyx dorsalis is described. We isolated two novel peptides Cd-125 and Cd-146 and a known peptide Thr(6)-bradykinin from only two venom sacs of solitary spider wasp Cyphononyx dorsalis without bioassay-guided fractionation. but instead guided by MALDI-TOF MS. The MALDI-TOF MS analysis of each fraction showed the purity and molecular weight of the components, which led to the isolation of the peptides virtually without loss of sample amount. The sequences of the novel peptides Cd-125 (Asp-Thr-Ala-Arg-Leu-Lys-Trp-His) and Cd-146 (Ser-Glu-Thr-Gly-Asn-Thr-Val-Thr-Val-Lys-Gly-Phe-Ser-Pro-Leu-Arg) were determined by Edman degradation together with mass spectrometry. and finally corroborated by solid-phase synthesis. The known peptide Thr(6)-bradykinin (Arg-Pro-Pro-Gly-Phe-Thr-Pro-Phe-Arg) was identified by comparison with the synthetic authentic specimen. This is the first example for any kinins to be found in Pompilidae wasp venoms. The procedure reported here can be applicable to studies on many other components of solitary wasp venoms with limited sample availability. (C) 2001 Elsevier B.V. Ltd. All rights reserved.

Peptídeos cíclicos hepatotóxicos: MALDI-TOF como uma ferramenta analítica

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Methodische Entwicklung der MALDI-TOF-Massenspektrometrie für Grenzbereiche der Makromolekülanalytik

Ziel dieser Arbeit war die methodische Entwicklung der Matrix-unterstützten Laserdesorptions/Ionisations- (MALDI-) Time-of-Flight- (TOF-) Massenspektrometrie (MS) zur Charakterisierung von Makromolekülen. Durch geeignete Experimente und unter Berücksichtigung der Ergebnisse ergänzender analytischer Methoden wurden neue Möglichkeiten der MALDI-TOF-MS-Methode erarbeitet, deren bisherige Grenzen genauer definiert und auf Basis eines besseren Verständnisses der limitierenden Faktoren in vielen Fällen auch überwunden.Die MALDI-Probenpräparation gestaltet sich generell sehr komplex. Es konnte gezeigt werden, dass die lösungsmittelfreie Probenpräparation die MALDI-Analytik in der Art verbessert, dass erzielte Ergebnisse qualitativ (z.B. Auflösung, Genauigkeit) und quantitativ (z.B. Reproduzierbarkeit) zuverlässiger sind. Wichtige Vorteile der lösungsmittelfreien MALDI-TOF-MS konnten bei einem breiten Spektrum unterschiedlicher Analyten herausgearbeitet werden. Fragmentierungslabile Analyte waren charakterisierbar, da weniger Laserleistung für den Desorptionsschritt in das Probengemisch eingebracht werden musste. Oxidationslabile bzw. thermolabile Substanzen (z.B. Pigmente) konnten charakterisiert werden, da auf den Löseschritt verzichtet werden konnte, der zu unerwünschten Veränderungen des Analyten führen kann. Generell konnte gezeigt werden, dass diese Probenpräparation geeignet ist, um schwer- und unlösliche Substanzen wie z.B. Poly(dithiathianthren)e und Poly(fluoren)e zu charakterisieren. Entmischungseffekte (z.B. bei Poly(etherimid)en und Poly(dimethylsiloxan)en), die in der konventionellen Probenpräparation während des Verdampfungsschrittes des Lösungsmittels zu einer inhomogenen Kristallisation des MALDI-Probengemisches führen, können überwunden werden, da vollständig auf Lösungsmittel verzichtet wird. So konnten beispielsweise nur durch den gezielten Einsatz der lösungsmittelfreien MALDI-TOF-MS Polystyrol-Proben analysiert werden, bei denen trotz optimierter Bedingungen die lösungsmittelbasierende MALDI-TOF-MS aufgrund unerwünschter Lösungsmitteleinflüsse fälschliche Ergebnisse lieferte. Die lösungsmittelfreie Probenpräparation ist eine wichtige Ergänzung zur Charakterisierung von Makromolekülen und erschließt neue Bereiche der Analytik, insbesondere bei unlöslichen Verbindungen und bei Analyt Matrix-Entmischungsphänomenen. Das bisherige Verständnis des zugrundeliegenden MALDI-Prozesses postuliert den homogenen Einbau des Analyten in den Matrixkristall. Die äußerst positiven experimentellen Ergebnisse der lösungsmittelfreien MALDI-TOF-MS widersprechen jedoch dieser Modellvorstellung, da bei der angewendeten Probenpräparation eine Homogenisierung auf molekularer Ebene auszuschließen ist. Durch die lösungsmittelfreie MALDI-TOF-MS am Modellanalyten Cytochrom C konnte nachgewiesen werden, dass der Einbau eines Analyten in einen Matrixkristall nicht zwingend notwendig, sondern aufgrund der erhöhten einzubringenden Laserleistung sogar eher von Nachteil ist. Der MALDI-Prozess verläuft umso effektiver, je geringer die (Rest)-Kristallinität und je inniger der Kontakt zwischen Analyt und Matrix sind. Methodische Aspekte der Fragmentionenanalyse wurden zunächst an einfachen Homopolymeren erarbeitet. Durch den gezielten Einsatz der MALDI-Fragmentionenanalytik konnte im Folgenden z.B. erstmals direkt die Sequenzanalyse eines statistischen Copolymers und eines Triblockcopolymers durchgeführt werden. Abschließend wurden bei anwendungsorientierten Untersuchungen zur Charakterisierung problematischer Analyten mittels MALDI-TOF-MS zunächst die individuellen Schwachstellen festgelegt. Durch geeignete Probenpräparations- und Messbedingungen wurde dann die MALDI-TOF-MS-Methode zur direkten Analyse schwer charakterisierbarer, labiler bzw. unlöslicher Analyten und Substanzgemische ermöglicht (z.B. Dendrimere, Polyzyklische Aromatische Kohlenwasserstoffe, umweltrelevantes Poly(vinylpyrrolidon)). Dabei wurden qualitative und quantitative Aspekte berücksichtigt. Außerdem wurden die analytischen Möglichkeiten und Limitierungen zur Charakterisierung von supramolekularen Komplexen anhand geeigneter Modellsysteme (z.B. Cyclodextrine) ermittelt.

Identification of animal Pasteurellaceae by MALDI-TOF mass spectrometry

Species of the family Pasteurellaceae play an important role as primary or opportunistic animal pathogens. In veterinary diagnostic laboratories identification of this group of bacteria is mainly done by phenotypic assays while genetic identification based on housekeeping genes is mostly used for research and particularly important diagnostic samples. MALDI-TOF MS seems to represent a promising alternative to the currently practiced cumbersome, phenotypic diagnostics carried out in many veterinary diagnostic laboratories. We therefore assessed its application for animal associated members of the family Pasteurellaceae. The Bruker Biotyper 3.0 database was complemented with reference spectra of clinically relevant as well as commensal animal Pasteurellaceae species using generally five strains per species or subspecies and tested for its diagnostic potential with additional, well characterized field isolates. About 250 strains comprising 15 genera and more than 40 species and subspecies were included in the study, covering most representatives of the family. A high discrimination at the genus and species level was observed. Problematic discrimination was only observed with some closely related species and subspecies. MALDI-TOF MS was shown to represent a highly potent method for the diagnosis of this group of animal pathogens, combining speed, precision and low running costs.

DNA sequencing and genotyping by transcriptional synthesis of chain-terminated RNA ladders and MALDI-TOF mass spectrometry

Sets of RNA ladders can be synthesized by transcription of a bacteriophage-encoded RNA polymerase using 3′-deoxynucleotides as chain terminators. These ladders can be used for sequencing of DNA. Using a nicked form of phage SP6 RNA polymerase in this study substantially enhanced yields of transcriptional sequencing ladders. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of chain-terminated RNA ladders allowed DNA sequence determination of up to 56 nt. It is also demonstrated that A→G and C→T variations in heterozygous and homozygous samples can be unambiguously identified by the mass spectrometric analysis. As a step towards single-tube sequencing reactions, α-thiotriphosphate nucleotide analogs were used to overcome problems caused by chain terminator-independent, premature termination and by the small mass difference between natural pyrimidine nucleotides.