Relevant bibliographies by topics / MALDI matrix

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Academic literature on the topic 'MALDI matrix'

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Published: 22 December 2023

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Journal articles on the topic "MALDI matrix"

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TANAKA, Koichi. "Preface: Issuing “MALDI Matrix”." Journal of the Mass Spectrometry Society of Japan 64, no. 5 (2016): 167. http://dx.doi.org/10.5702/massspec.s16-34.

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Fukuyama, Yuko. "MALDI Matrix Research for Biopolymers." Mass Spectrometry 4, no. 1 (2015): A0037. http://dx.doi.org/10.5702/massspectrometry.a0037.

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Martic, Sanela, John D. Brennan, Michael A. Brook, Suzanne Ackloo, and Noemi Nagy. "Towards the development of a covalently tethered MALDI system — A study of allyl-modified MALDI matrixes." Canadian Journal of Chemistry 85, no. 1 (January 1, 2007): 66–76. http://dx.doi.org/10.1139/v06-185.

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An emerging application of matrix-assisted laser desorption ionization (MALDI) mass spectrometry is the analysis of low molecular weight (LMW) compounds, often via coupled liquid chromatography — MALDI-MS methods. However, in many cases, the low molecular weight region of MALDI mass spectra is obscured by the presence of signals originating from the matrix, suggesting that the development of tethered MALDI matrixes may be required to optimize MS performance for such compounds. To gain insight into potential sites for covalent attachment of MALDI matrixes, we have systematically investigated the role played by a variety of functional group motifs in determining matrix efficiency for three common MALDI matrixes, as judged both by total signal intensity and background noise from matrix decomposition for a set of LMW compounds. A series of allyl derivatives of standard matrixes was prepared, and the efficiency of these materials in the MALDI experiment was measured. All modifications of established matrixes, e.g., 2,5-dihydroxybenzoic acid (DHB), α-cyano-4-hydroxycinnamic acid (CHCA), and caffeic acid (CA), or close analogues led to decreased absolute signal intensity and signal-to-background levels. Improved performance was generally observed with (i) the presence of a phenolic group (carboxylic acids were less effective) (ii) crystalline derivatives, and (iii) compounds that had high extinction coefficients at wavelengths near to that of the exciting laser (337 nm). The most interesting derivatives were the O-allyl ether (15) and N-allyl amide (16) of caffeic acid. These compounds did not facilitate signals from all four analytes tested. However, the observed spectra contained fewer signals from the matrix than from the parent compound CA. These compounds demonstrate that functionalization of MALDI matrixes, ultimately leading to tethered matrixes, is possible without jeopardizing signal intensity.Key words: MALDI, protected matrix, phenol, caffeic acid, allyl ether.
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Gorbunov A. Yu. and Podolskaya E. P. "Fabrication of nanoscale multimolecular structures of lanthanum stearate using Langmuir monolayers for laser desorption/ionization mass spectrometry." Technical Physics Letters 48, no. 11 (2022): 29. http://dx.doi.org/10.21883/tpl.2022.11.54885.19320.

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Matrix-assisted laser desorption/ionization (MALDI) from the surface of nanosized multimolecular structures based on lanthanum stearate monolayers (FLa) has been studied. The presence of FLa on the surface of MALDI target was confirmed experimentally by laser desorption of lanthanum-containing organic ions. MALDI target functionalization with FLa is shown to significantly increase the yield of target peptide ions, with the optimum being achieved at a film thickness of about 6 monolayers. An approach is proposed in a "lab-on-a-plate" format, which allows specific extraction of peptides modified with chlorine-containing compounds and includes the following steps: functionalization of the target surface, metal affinity extraction, matrix deposition and MALDI mass spectrometric analysis. Keywords: mass spectrometry, matrix assisted laser desorption/ionization (MALDI), surface, Langmuir monolayers, metal affinity chromatography.
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Montaudo, Giorgio, Filippo Samperi, Maurizio S. Montaudo, Sabrina Carroccio, and Concetto Puglisi. "Current Trends in Matrix-Assisted Laser Desorption/Ionization of Polymeric Materials." European Journal of Mass Spectrometry 11, no. 1 (February 2005): 1–14. http://dx.doi.org/10.1255/ejms.718.

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In the last few years, mass spectrometry has rapidly become indispensable in polymer analysis and complements, in many ways, the structural data provided by nuclear magnetic resonance. Mass spectrometry of polymers is emerging as a revolutionary technique, capable of challenging the techniques and protocols established for years for the characterization of synthetic polymers. Matrix-assisted laser desorption/ionization (MALDI) has become a widely applied method for the structural characterization of synthetic polymers. The primary aim of this review is to illustrate some recent advances in the study of macromolecular systems by MALDI. MALDI allows the identification of repeat units and end groups, the structural analysis of linear and cyclic oligomers and the estimate of composition and sequence for co-polymers. MALDI is also quite useful for the measurement of molar mass and bivariate distributions in polymers and for the detection of self-association in macromolecules, performed by coupling MALDI with size exclusion chromatography (SEC). Recently MALDI has been applied, with remarkable success, to the study of thermal and oxidative processes in polymers and to the characterization of co-polymers obtained by reactive polymer blending. Selected applications of MALDI to polymers are illustrated herewith.
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Lippa, Timothy, Nelli I. Taranenko, Coorg R. Prasad, and Vladimir M. Doroshenko. "Infrared Matrix-Assisted Laser Desorption/Ionization Quadrupole Ion Trap Mass Spectrometry." European Journal of Mass Spectrometry 8, no. 3 (June 2002): 263–71. http://dx.doi.org/10.1255/ejms.498.

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Performance characteristics of an infrared (IR) matrix-assisted laser desorption/ionization (MALDI) quadrupole ion trap (QIT) mass spectrometer are presented. Both an IR laser and an ultraviolet (UV) laser have been coupled to the MALDI ion source, allowing for a comparative study of the spectra obtained for the same analyte molecules taken at these two wavelengths. The mass range of the QIT instrument was extended by operating it at a frequency as low as 200 kHz. The results presented for small and medium-size peptides demonstrated a lesser degree of analyte ion fragmentation in the case of the IR-MALDI source compared with that obtained using the UV-MALDI source. Due to the fragmentation phenomenon, the mass resolution for cytochrome C ions(MW12384 Da) was an order of a magnitude higher in the case of IR-MALDI compared with the use of UV-MALDI. This phenomenon has been shown to effect the calibration of the trap instrument for higher masses.
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Fresnais, Margaux, Esra Yildirim, Seda Karabulut, Dirk Jäger, Inka Zörnig, Julia Benzel, Kristian W. Pajtler, et al. "Rapid MALDI-MS Assays for Drug Quantification in Biological Matrices: Lessons Learned, New Developments, and Future Perspectives." Molecules 26, no. 5 (February 26, 2021): 1281. http://dx.doi.org/10.3390/molecules26051281.

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Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has rarely been used in the field of therapeutic drug monitoring, partly because of the complexity of the ionization processes between the compounds to be quantified and the many MALDI matrices available. The development of a viable MALDI-MS method that meets regulatory guidelines for bioanalytical method validation requires prior knowledge of the suitability of (i) the MALDI matrix with the analyte class and properties for ionization, (ii) the crystallization properties of the MALDI matrix with automation features, and (iii) the MS instrumentation used to achieve sensitive and specific measurements in order to determine low pharmacological drug concentrations in biological matrices. In the present hybrid article/white paper, we review the developments required for the establishment of MALDI-MS assays for the quantification of drugs in tissues and plasma, illustrated with concrete results for the different steps. We summarize the necessary parameters that need to be controlled for the successful development of fully validated MALDI-MS methods according to regulatory authorities, as well as currently unsolved problems and promising ways to address them. Finally, we propose an expert opinion on future perspectives and needs in order to establish MALDI-MS as a universal method for therapeutic drug monitoring.
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Israr, Muhammad Zubair, Dennis Bernieh, Andrea Salzano, Shabana Cassambai, Yoshiyuki Yazaki, and Toru Suzuki. "Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications." Clinical Chemistry and Laboratory Medicine (CCLM) 58, no. 6 (June 25, 2020): 883–96. http://dx.doi.org/10.1515/cclm-2019-0868.

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AbstractBackgroundMatrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics.ContentThis review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories.SummaryMALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases.OutlookThere is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.
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Creaser, Colin S., James C. Reynolds, Andrew J. Hoteling, William F. Nichols, and Kevin G. Owens. "Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionisation Ion Trap Mass Spectrometry of Synthetic Polymers: A Comparison with Vacuum Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry." European Journal of Mass Spectrometry 9, no. 1 (February 2003): 33–44. http://dx.doi.org/10.1255/ejms.528.

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Atmospheric pressure matrix-assisted laser desorption/ionisation quadrupole ion trap (AP-MALDI/QIT) mass spectrometry has been investigated for the analysis of polyethylene glycol (PEG 1500) and a hyperbranched polymer (polyglycidol) in the presence of alkali–metal salts. Mass spectra of PEG 1500 obtained at atmospheric pressure showed dimetallated matrix/analyte adducts, in addition to the expected alkali–metal/PEG ions, for all matrix/alkali–metal salt combinations. The relative intensities of the desorbed ions were dependent on the matrix, the alkali–metal salt added to aid cationisation and the ion trap interface conditions [capillary temperature, in-source collisionally-induced dissociation (CID)]. These data indicate that the adducts are rapidly stabilised by collisional cooling enabling them to be transferred into the ion trap. Experiments using identical sample preparation conditions were carried out on a vacuum MALDI time-of-flight (ToF) mass spectrometer. In all cases, vacuum MALDI-ToF spectra showed only alkali–metal/PEG ions and no matrix/analyte adducts. The tandem mass spectrometry (MS/MS) capability of the ion trap has been demonstrated for a lithiated polyglycol yielding a rich fragment-ion spectrum. Analysis of the hyperbranched polymer polyglycidol by AP-MALDI/QIT reveals the characteristic ion series for these polymers as also observed under vacuum MALDI-ToF conditions.
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Flensburg, John, Anders Tangen, Maria Prieto, Ulf Hellman, and Henrik Wadensten. "Chemically-Assisted Fragmentation Combined with Multi-Dimensional Liquid Chromatography and Matrix-Assisted Laser Desorption/Ionization Post Source Decay, Matrix-Assisted Laser Desorption/Ionization Tandem Time-of-Flight or Matrix-Assisted Laser Desorption/Ionization Tandem Mass Spectrometry for Improved Sequencing of Tryptic Peptides." European Journal of Mass Spectrometry 11, no. 2 (April 2005): 169–79. http://dx.doi.org/10.1255/ejms.734.

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Derivatization of tryptic peptides using an Ettan CAF matrix-assisted laser desorption/ionization (MALDI) sequencing kit in combination with MALDI-post source decay (PSD) is a fast, accurate and convenient way to obtain de novo or confirmative peptide sequencing data. CAF (chemically assisted fragmentation) is based on solid-phase derivatization using a new class of water stable sulfonation agents, which strongly improves PSD analysis and simplifies the interpretation of acquired spectra. The derivatization is performed on solid supports, ZipTipμC18, limiting the maximum peptide amount to 5 μg. By performing the derivatization in solution enabled the labeling of tryptic peptides derived from 100 μg of protein. To increase the number of peptides that could be sequenced, derivatized peptides were purified using multidimensional liquid chromatography (MDLC) prior to MALDI sequencing. Following the first dimension strong cation exchange (SCX) chromatography step, modified peptides were separated using reversed-phase chromatography (RPC). During the SCX clean up step, positively charged peptides are retained on the column while properly CAF-derivatized peptides (uncharged) are not. A moderately complex tryptic digest, prepared from six different proteins of equimolar amounts, was CAF-derivatized and purified by MDLC. Fractions from the second dimension nano RPC step were automatically sampled and on-line dispensed to MALDI sample plates and analyzed using MALDI mass spectrometry fragmentation techniques. All proteins in the derivatized protein mixture digest were readily identified using MALDI-PSD or MALDI tandem mass spectrometry (MS/MS). More than 40 peptides were unambiguously sequenced, representing a seven-fold increase in the number of sequenced peptides in comparison to when the CAF-derivatized protein mix digest was analyzed directly (no MDLC-separation) using MALDI-PSD. In conclusion, MDLC purification of CAF-derivatized peptides significantly increases the success rate for de novo and confirmative sequencing using various MALDI fragmentation techniques. This new approach is not only applicable to single protein digests but also to more complex digests and could, thus, be an alternative to electrospray ionization MS/MS for peptide sequencing.
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Dissertations / Theses on the topic "MALDI matrix"

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Krüger, Ralf. "Untersuchungen zum Einbau von Analytionen in MALDI-Matrizes sowie zur Ionisation und Adduktbildung in der MALDI-Massenspektrometrie." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969681682.

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Bouschen, Werner. "Ortsaufgelöste MALDI-Massenspektrometrie an biologischen und synthetischen Oberflächen." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971766886.

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Jacksén, Johan. "Improved techniques for CE-MALDI-MS off-line coupling and MALDI-MS analysis of primarily hydrophobic proteins and peptides." Licentiate thesis, KTH, Chemistry, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4599.

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Due to the hydrophobic nature of integral membrane proteins (IMP) they give rise to several difficulties concerning handling and analysis, which is not the case for the most water soluble proteins. New analysis methods are needed, where the insolubility problems of the hydrophobic proteins due to aggregation and adhesion are tackled. Those problems also affect digestion performance and equipment compatibility for the analysis.

Protocols for analysis and separation specified for IMP are presented in Paper I and III.

The instrumentation used in this work was capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Both instruments are suitable for peptide/proteins analysis.

In Paper I, protocols for a CE separation of bacteriorhodopsin (BR) peptides as model IMP peptides are established. Also, a partially automated manufacturing procedure of a concentration MALDI-target is presented, suitable for fractions from CE. The MS analysis detected 9 out of 10 cyanogen bromide (CNBr) digested BR peptides. A novel technique for the off-line integration of CE to MALDI-MS using a closed-open-closed system is presented in Paper II, where the open part is a microcanal functioning as a MALDI target window. Investigation of the microcanal electro-osmotic flow (EOF) properties and band broadening characteristics was performed. A protein separation was obtained and detected with MALDI-MS analysis in the microcanal. Different protein digestion methods were evaluated using BR in Paper III through MALDI-MS. Several digestion methods as well as MS media were investigated alongside different MALDI matrices. For example, matrices as the hydrophobic 2,6-dihydroxyacetophenone (DHAP) and 2-Hydroxy-3-methoxybenzoic acid (2H3MBA) or 2-Hydroxy-5-methoxybenzoic acid (2H5MBA) mixed with DHB, appeared to be promising matrices for analysis of BR.


Med anledning av integrala membranproteiners (IMP) hydrofoba egenskaper uppstår flera svårigheter vid hantering och analys av IMP, vilket inte är fallet för vattenlösliga proteiner. Nya analysmetoder krävs, som löser löslighetsproblemen för de hydrofoba proteinerna som tex flockning och adsorbtion. Dessa problem påverkar även klyvningsgrad och kompatibilitet med analysutrustningen.

I Artikel I och Artikel III presenteras protokoll för analys och separation specifikt för IMP. Instrumenteringen som har använts i detta arbete är kapillärelektrofores (CE) och matris-assisterad laserdesorptions-joniserings-masspektrometri (MALDI-MS). Båda instrumenten är lämpade för peptid/protein analyser.

I Artikel I, presenteras protokoll för en CE separation av peptider från bacteriorhodopsin (BR), som användes som modellpeptider för IMP. En delvis automatiserat tillverkningsprocedur för en koncentrerande MALDI-platta, som är anpassad för CE fraktionerna beskrivs också. MS-analysen detekterade 9 av 10 BR-peptider från cyanobromid-klyvning (CNBr). En ny teknik för off line-integrering av CE till MALDI-MS genom ett slutet-öppet-slutet system presenteras i Artikel II, där den öppna delen är en mikrokanal som fungerar som detektionsfönster i MALDI. Undersökning av mikrokanalens egenskaper som tex det elektroosmotiska flödet (EOF) och bandbreddningen utvärderades. En proteinseparation genomfördes och detekterades med MALDI–MS i mikrokanalen. Olika proteinklyvningsmetoder för BR undersöktes i Artikel III med MALDI-MS. Flera proteinklyvningsmetoder samt MS-medier utvärderades tillsammans med olika MALDI-matriser. Den hydrofoba matrisen 2,6-dihydroxyacetophenone (DHAP) och 2-Hydroxy-3-methoxybenzoic acid (2H3MBA) eller 2-Hydroxy-5-methoxybenzoic acid (2H5MBA) blandade med DHB, visade sig exempelvis vara lovande matriser för BR-analyser.

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Priyasantha, Kandalama KD. "DEVELOPMENT OF A NOVEL MATRIX ASSISTED LASER DESORPTION / IONIZATION (MALDI) BASED PEPTIDE QUANTITATION APPROACH." OpenSIUC, 2015. https://opensiuc.lib.siu.edu/dissertations/989.

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Matrix Assisted Laser Desorption / Ionization (MALDI) Mass Spectrometry (MS) has emerged as an important tool in the field of proteomics mainly because it is simple, quick and efficient. The identification and quantitation of biomarkers, protein targets for drugs, and metabolites are some of the important fields in proteomics research. Although MALDI MS is an important tool in proteomics research there are drawbacks of the technique that need further development in order for the approach to be used in clinical laboratories. One major limitation of MALDI MS is the generally poor reproducibility of ion signal intensities, which negatively impacts the quantitation of peptides and protein by MALDI MS. A considerable amount of research has been performed in an effort to improve the ion signal reproducibility in MALDI MS. However, many of the approaches developed have introduced specific drawbacks with respect to the traditional dried-droplet sample preparation technique, negating many of the advantages of the MALDI MS approach. This project has focused on the development of a novel approach to quantify peptides by MALDI MS while preserving traditional known advantages of the technique. The studies performed show that an approach in which the ion signal base widths are manipulated to match that of a reference ion signal, through adjustments in desorption laser intensity, leads to much higher reproducibility in the integrated ion signal intensities. A standard curve acquired using the constant ion signal base width approach showed lower average RSDs (< 10.00% vs.> 39.00%) and improved R2 values (> 0.9600 vs. < 0.809) as compared to the conventional constant desorption laser intensity approach. Subsequent work also revealed that the peptide hydrophobic / hydrophilic properties influenced the applicability of the quantitation approach to mixtures of peptides. Specifically, the data revealed that peptides with differing hydrophobic / hydrophilic properties appear to co-crystallize with the MALDI matrix differently leading to an inability to use a hydrophobic peptide signal to quantitate a hydrophilic peptide, and vice versa. This latter conclusion was further supported in similar studies performed on the mixture of peptides resulting from tryptic digestion of the protein bovine serum albumin.
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Allwood, Daniel Anthony. "Characterisation and ionisation modelling of matrices in MALDI mass spectrometry." Thesis, University of Hull, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301477.

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PENG, LIJUAN. "MATRIX-ASSISTED LASER DESORPTION/IONIZATION (MALDI) TARGET MODIFICATION FOR ENHANCED PROTEOMICS ANALYSIS AND PLASMA POLYMER CHARACTERIZATION BY MALDI MASS SPECTROMETRY." OpenSIUC, 2010. https://opensiuc.lib.siu.edu/dissertations/207.

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The work described in this dissertation is divided into three sections. In the first section three surface modifications are used to produce MALDI targets having reduced surface-protein binding affinity with a goal of increasing peptide/protein MALDI ion signals and lowering the limits of detection (LODs) for proteins and peptides. The second section discusses a bioselective MALDI target, produced via radio frequency (rf) plasma deposited ethylenediamine (EDA), for on-target separation of complex protein mixtures. The third section develops a new approach for characterization of rf plasma-deposited bulk polymers by using MALDI MS. Previous studies in our group have shown that the analyte signal in a MALDI MS experiment is strongly influenced by the binding interactions between the target surface and the analyte. Specifically, the analyte signal increases with decreasing surface-analyte binding affinity, which has been attributed to more unbound analyte being available for incorporation within the MALDI matrix. In the presented studies MALDI targets are modified with polyethylene glycol (PEG)-like structures via chemical grafting of PEG onto polyurethane (PU) film and rf plasma polymerization of ethylene oxide vinyl ether (EO2) and tetraglyme. It is shown that there are enhancements in the protein MALDI ion signals on these modified targets and that the LOD for target proteins is decreased by a factor of 2-10 in comparison with the conventional stainless steel MALDI target. On-probe affinity capture (OPAC) MALDI MS, developed in our group, has shown that functional group modified MALDI targets can be used to rapidly and selectively isolate target analytes from complex samples. For applications involving analysis of complex peptide/protein mixtures, fractionation of the mixture on the basis of component pI can reduce MALDI ion suppression effects leading to efficient ionization of larger numbers of mixture components. In the present studies a MALDI target is modified by rf plasma deposition of polymerized EDA to yield an OPAC target suitable for capture of proteins with low pI (expected to be negatively charged at neutral pH). In subsequent MALDI MS analyses of both control and biological mixtures after fractionation on the OPAC target it is observed that a significant number of additional peptide/protein ion signals are detected. The results of these studies, along with studies of the effects of the density of the primary amine functionality on the bio-selective MALDI ion signals, are presented. The complex nature of the polymer films resulting from plasma polymerization makes it very difficult to characterize their molecular structures. The presented study is the first to use MALDI MS for characterization of rf plasma-deposited bulk polymers and for investigation of the rf plasma polymerization process. It is shown that the mass spectra of the soluble fraction of allyl alcohol, EO2 and ethylene glycol butyl vinyl ether -plasma polymers contain clear polymer series. Furthermore, it is found that the peaks of the EO2-plasma polymer series shift to higher molecular weight distribution with decreasing plasma duty cycle. In contrast to predictions based on conventional radical polymerization, the mass spectra of all three plasma polymers exhibit the same repeat unit of 44 Da, for which the most likely structure would be -(CH2CH2O)-.
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Walbrodt, Dirk [Verfasser]. "Das Ablationsverhalten von Matrix- und Analytneutralen im UV-MALDI-Prozess / Dirk Walbrodt." Kiel : Universitätsbibliothek Kiel, 2008. http://d-nb.info/101955360X/34.

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Tummala, Manorama. "Surfactant-Aided Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (SA-MALDI MS)." University of Cincinnati / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1100672049.

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Siricord, Cornelia Charito. "Detection of Phytophthora species by MALDI-TOF mass spectrometry." Thesis, Siricord, Cornelia Charito (2005) Detection of Phytophthora species by MALDI-TOF mass spectrometry. PhD thesis, Murdoch University, 2005. https://researchrepository.murdoch.edu.au/id/eprint/314/.

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Phytophthora diseases have caused worldwide economic, social and environmental impacts for decades. Once their presence is confirmed, they are difficult to eradicate. To reduce and manage the damage inflicted by the pathogen, fast and reliable disease management protocols are required. Tests that enable the rapid and reliable identification of the pathogen assist greatly in disease management. Phytophthora species are traditionally not only detected by baiting but also by plating of symptomatic tissue on selective media. Species can be identified by the characteristics of the mycelium growing out of the bait. However, the method is low throughput, labour intensive, and prone to false negatives. An alternative approach would be to detect the pathogen by the presence of its DNA. This involves amplification of the pathogen DNA using Polymerase Chain Reaction (PCR) and detection of the amplification product. Detection is usually by agarose gel electrophoresis. However, this is also a labour intensive process involving pouring, loading, running, and staining of the gels. The aim of this thesis is to explore the use of Matrix Assisted Laser Desorption/ Ionisation Time-of-Flight (MALDI-TOF) mass spectrometry for detection of PCR products. This procedure enables the analysis of large numbers of samples within a very short time-frame as the average time for analysis of each sample is in the order of milliseconds. The assay involves annealing an extension (genotyping) primer to the PCR product and its extension by a single nucleotide. The nature of the nucleotide added differentiates species as does the site to which the primer anneals. Multiple extension (genotyping) primers can be used together in a single reaction for detection of multiple species. In this project four genotyping primers (GPs) were designed from the ITS regions of Phytophthora palmivora, Phytophthora cinnamomi, Phytophthora citricola, and Phytophthora cambivora. The extension primers were tested for their specificity on the DNA of the target species. The four primers designed were specific for their intended targets except for GPpalm3 which in addition to being extended by ddT when tested with DNA from P. palmivora, was also extended by ddC when tested with DNA from other species of Phytophthora or Pythium. These primers were also tested for their ability to detect multiple Phytophthora species in a single reaction (multiplexing). Mixtures of primers were added to mixed DNA templates and the primer extension reaction carried out. The primers were designed so that their masses were sufficiently different for them to be identified from a mixture. Six replicates were analysed for each reaction. In general only about 1-3 of the six replicates gave a positive reaction. This indicates that there may be some interference between primers, or that the presence of all four nucleotides interfered with the primer extension reaction. Increasing either the amount of enzyme, the amount of nucleotides or both did not improve the results. The sensitivity of detection was tested by the addition of different amounts of mycelium to soil. The detection sensitivity depended on the primer pair used for PCR amplification. The ITS1/2 primer pair was more sensitive than the ITS1/4 pair. The limit of detection was 1 mcg mycelium g soil-1. However using nested PCR, levels of sensitivity comparable to those obtained using the ITS1/2 primer pair could be achieved. Primers to other regions of the genome such as the beta cinnamomin elicitin gene gave very low levels of sensitivity compared to the ITS primers. In comparison with DNA detection we found that the limit of detection using baiting was 4 mcg mycelium g soil-1. Results below this limit were unreliable. The method suffered from the additional disadvantage that it took a long time in comparison to DNA detection. DNA detection methods do not distinguish between living and dead organisms in the soil. However it can be hypothesised that DNA is unlikely to persist for any significant length of time in soil. To test this, we added plasmid DNA to soil and tested the persistence of this DNA using a variety of methods such as precipitation of labelled DNA, southern blotting and PCR amplification. It was found that in general, in soils from different ecosystems, the bulk of the DNA was undetectable after 24 hours. The rate of DNA breakdown differed with the soil type. In some soils, the added DNA was not detected even after 2 hours, whereas in others it could be observed after 10 hours. The detection depended on the method. Southern blotting showed that although DNA could be observed at 10 hours, by 24 hours it was completely degraded. In contrast a PCR product could be obtained from the soil extracts up to 24 hours. In a separate experiment, plasmid DNA was detectable over a 24 hour incubation period in 5 soil samples from 5 different sites. The results suggest that DNA is degraded rapidly in soil and is unlikely to persist longer than 24 hours. The results in this thesis demonstrate that MALDI-TOF MS is a suitable alternative to agarose gel electrophoresis for analysis of PCR products. The technique is rapid, differentiates species from mixtures, is high-throughput and amenable to automation. Implementation will require further research to automate the primer extension assay to reduce the sensitivity to impurities in the DNA and to design parameters for sampling asymptomatic material.
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Siricord, Cornelia Charito. "Detection of Phytophthora species by MALDI-TOF mass spectrometry." Siricord, Cornelia Charito (2005) Detection of Phytophthora species by MALDI-TOF mass spectrometry. PhD thesis, Murdoch University, 2005. http://researchrepository.murdoch.edu.au/314/.

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Phytophthora diseases have caused worldwide economic, social and environmental impacts for decades. Once their presence is confirmed, they are difficult to eradicate. To reduce and manage the damage inflicted by the pathogen, fast and reliable disease management protocols are required. Tests that enable the rapid and reliable identification of the pathogen assist greatly in disease management. Phytophthora species are traditionally not only detected by baiting but also by plating of symptomatic tissue on selective media. Species can be identified by the characteristics of the mycelium growing out of the bait. However, the method is low throughput, labour intensive, and prone to false negatives. An alternative approach would be to detect the pathogen by the presence of its DNA. This involves amplification of the pathogen DNA using Polymerase Chain Reaction (PCR) and detection of the amplification product. Detection is usually by agarose gel electrophoresis. However, this is also a labour intensive process involving pouring, loading, running, and staining of the gels. The aim of this thesis is to explore the use of Matrix Assisted Laser Desorption/ Ionisation Time-of-Flight (MALDI-TOF) mass spectrometry for detection of PCR products. This procedure enables the analysis of large numbers of samples within a very short time-frame as the average time for analysis of each sample is in the order of milliseconds. The assay involves annealing an extension (genotyping) primer to the PCR product and its extension by a single nucleotide. The nature of the nucleotide added differentiates species as does the site to which the primer anneals. Multiple extension (genotyping) primers can be used together in a single reaction for detection of multiple species. In this project four genotyping primers (GPs) were designed from the ITS regions of Phytophthora palmivora, Phytophthora cinnamomi, Phytophthora citricola, and Phytophthora cambivora. The extension primers were tested for their specificity on the DNA of the target species. The four primers designed were specific for their intended targets except for GPpalm3 which in addition to being extended by ddT when tested with DNA from P. palmivora, was also extended by ddC when tested with DNA from other species of Phytophthora or Pythium. These primers were also tested for their ability to detect multiple Phytophthora species in a single reaction (multiplexing). Mixtures of primers were added to mixed DNA templates and the primer extension reaction carried out. The primers were designed so that their masses were sufficiently different for them to be identified from a mixture. Six replicates were analysed for each reaction. In general only about 1-3 of the six replicates gave a positive reaction. This indicates that there may be some interference between primers, or that the presence of all four nucleotides interfered with the primer extension reaction. Increasing either the amount of enzyme, the amount of nucleotides or both did not improve the results. The sensitivity of detection was tested by the addition of different amounts of mycelium to soil. The detection sensitivity depended on the primer pair used for PCR amplification. The ITS1/2 primer pair was more sensitive than the ITS1/4 pair. The limit of detection was 1 mcg mycelium g soil-1. However using nested PCR, levels of sensitivity comparable to those obtained using the ITS1/2 primer pair could be achieved. Primers to other regions of the genome such as the beta cinnamomin elicitin gene gave very low levels of sensitivity compared to the ITS primers. In comparison with DNA detection we found that the limit of detection using baiting was 4 mcg mycelium g soil-1. Results below this limit were unreliable. The method suffered from the additional disadvantage that it took a long time in comparison to DNA detection. DNA detection methods do not distinguish between living and dead organisms in the soil. However it can be hypothesised that DNA is unlikely to persist for any significant length of time in soil. To test this, we added plasmid DNA to soil and tested the persistence of this DNA using a variety of methods such as precipitation of labelled DNA, southern blotting and PCR amplification. It was found that in general, in soils from different ecosystems, the bulk of the DNA was undetectable after 24 hours. The rate of DNA breakdown differed with the soil type. In some soils, the added DNA was not detected even after 2 hours, whereas in others it could be observed after 10 hours. The detection depended on the method. Southern blotting showed that although DNA could be observed at 10 hours, by 24 hours it was completely degraded. In contrast a PCR product could be obtained from the soil extracts up to 24 hours. In a separate experiment, plasmid DNA was detectable over a 24 hour incubation period in 5 soil samples from 5 different sites. The results suggest that DNA is degraded rapidly in soil and is unlikely to persist longer than 24 hours. The results in this thesis demonstrate that MALDI-TOF MS is a suitable alternative to agarose gel electrophoresis for analysis of PCR products. The technique is rapid, differentiates species from mixtures, is high-throughput and amenable to automation. Implementation will require further research to automate the primer extension assay to reduce the sensitivity to impurities in the DNA and to design parameters for sampling asymptomatic material.
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Books on the topic "MALDI matrix"

1

Liang, Li, ed. MALDI mass spectrometry for synthetic polymers analysis. Hoboken: Wiley, 2010.

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Pirone, Ciro. MADI movimento internazionale: Madi la materia del tempo. Fisciano]: Gutenberg edizioni, 2017.

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Malgras, Denis. Quel usage des plantes médicinales au Mali aujourd'hui? Bamako, Mali: Centre Djoliba, 1993.

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Ch'aga pŏsŏt ŭro malgi am igyŏnaegi: Kajŏng esŏ silch'ŏn hanŭn Ch'aga pŏsŏt chayŏn yopŏp. [Seoul]: Kanasel Puk, 2009.

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Charles, Bailleul, ed. Richesses médicinales du Bénin, Burkina Faso, Mali, Sénégal, Togo--: Pays de la zone sahélo-soudano-guinéenne. Bamako: Donniya, 2009.

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Hillenkamp, Franz, and Jasna Peter-Katalinic. Maldi MS: A Practical Guide to Instrumentation, Methods and Applications. Wiley & Sons, Incorporated, John, 2013.

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Hillenkamp, Franz, and Jasna Peter-Katalinic. Maldi MS: A Practical Guide to Instrumentation, Methods and Applications. Wiley & Sons, Limited, John, 2007.

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Hillenkamp, Franz, and Jasna Peter-Katalinic. Maldi MS: A Practical Guide to Instrumentation, Methods and Applications. Wiley & Sons, Incorporated, John, 2013.

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Hillenkamp, Franz, and Jasna Peter-Katalinic. Maldi MS: A Practical Guide to Instrumentation, Methods and Applications. Wiley & Sons, Limited, John, 2013.

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Hillenkamp, Franz, and Jasna Peter-Katalinic. Maldi MS: A Practical Guide to Instrumentation, Methods and Applications. Wiley & Sons, Incorporated, John, 2013.

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Book chapters on the topic "MALDI matrix"

1

O'Connor, Peter B. "The Development of Matrix-Assisted Laser Desorption/Ionization Sources." In Electrospray and MALDI Mass Spectrometry, 185–213. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9780470588901.ch6.

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Mathur, Sonal, Alexis Nazabal, and Renato Zenobi. "Probing Noncovalent Interactions by Electrospray Ionization and Matrix-Assisted Laser Desorption/Ionization." In Electrospray and MALDI Mass Spectrometry, 535–70. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9780470588901.ch15.

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Santos, Cledir, Paula Galeano, Reginaldo Lima Neto, Manoel Marques Evangelista Oliveira, and Nelson Lima. "MALDI-TOF MS and its requirements for fungal identification." In Trends in the systematics of bacteria and fungi, 119–40. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0119.

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Abstract Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is now used as a routine technique for the fast and reliable identification of fungi at the species level and, currently, it represents an important phenotypic methodology based on proteomic profiles. The main limitations to MALDI-TOF MS for fungal identification are related to sample quality (e.g. quality of biological material such as rigidity or pigmentation of cell walls), sample preparation (e.g. the myriad of sample preparation methodologies that deliver different data sets to different MALDI-TOF MS databases) and the databases themselves (e.g. the 'black-box' commercial databases). This chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed.
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Karas, M., and U. Bahr. "Matrix-Assisted Laser Desorption-Ionization (MALDI) Mass Spectrometry of Biological Molecules." In Mass Spectrometry in Biomolecular Sciences, 33–49. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0217-6_2.

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Karas, M., and U. Bahr. "Matrix-Assisted Laser Desorption-Ionization (MALDI) Mass Spectrometry: Principles and Applications." In Selected Topics in Mass Spectrometry in the Biomolecular Sciences, 33–53. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5165-8_3.

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Dilmetz, Brooke A., Peter Hoffmann, and Mark R. Condina. "Quantitative Approach Using Matrix-Assisted Laser Desorption/ Time-of-Flight (MALDI-ToF) Mass." In Methods in Molecular Biology, 159–66. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_12.

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Bashir, Sajid, Jingbo Liu, and Peter J. Derrick. "Hydrophilic/Phobic Tailored Multi-laned/Layer Matrix-Assisted Laser Desorption/Ionization (HTML-MALDI)." In Advanced Materials for Multidisciplinary Applications, 339–55. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-39404-1_13.

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Chen, Yanfeng, Ying Liu, Jeremy Allegood, Elaine Wang, Begoña Cachón-González, Timothy M. Cox, Alfred H. Merrill, and M. Cameron Sullards. "Imaging MALDI Mass Spectrometry of Sphingolipids Using an Oscillating Capillary Nebulizer Matrix Application System." In Methods in Molecular Biology, 131–46. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-746-4_7.

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Mack, P., F. Widmer, and M. Duncan. "Analysis of peptide-protein conjugates by matrix-assisted laser desorption ionization (MALDI) mass spectrometry." In Peptides 1994, 406–7. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-1468-4_182.

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Macha, Stephen F., and Patrick A. Limbach. "Analysis of Polymeric Hydrocarbon Materials by Matrix-Assisted Laser Desorption/Ionization (Maldi) Mass Spectrometry." In Analytical Advances for Hydrocarbon Research, 385–404. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4419-9212-3_16.

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Conference papers on the topic "MALDI matrix"

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Murray, Kermit K., Michelle D. Beeson, and David H. Russell. "Laser Ionization of Biomolecules in Solution." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.tha.5.

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Many powerful laser based methods are unavailable for the analysis of molecules in solution. Techniques for the analysis of liquids are particularly important for the study of biomolecules, whose natural environment is a water solution. Mass spectrometry is a powerful analytical technique, but liquids and mass spectrometers are fundamentally incompatible. We have developed a technique for laser ionization of biomolecules in solution by applying matrix-assisted laser desorption ionization (MALDI) to liquid aerosols. In the typical MALDI experiment, the analyte biomolecule is deposited from solution onto a metal surface with a 100 to 50,000 molar excess of a suitable matrix, usually a UV absorbing organic acid.1 The solvents are allowed to evaporate and the sample is inserted into the source region of a mass spectrometer. Light from a pulsed laser is absorbed by the matrix causing both ablation of the surface and ionization of the intact biomolecule. In the aerosol MALDI experiment, 2,3 the analyte biomolecule is dissolved in a methanol solution with an ultraviolet absorbing matrix. The aerosol is sprayed into vacuum, desolvated, and ionized by pulsed UV laser radiation. The ions are mass separated in a time-of-flight (TOF) mass spectrometer. Aerosol MALDI mass spectra have been obtained for a variety of peptides and proteins with molecular weights as large as 80,000. We have used aerosol MALDI as a liquid chromatography detection method4 (LC/MS) and as a probe of aerosol and cluster chemistry.5 This paper gives a general description of aerosol MALDI and discusses some recent results for peptide and protein ionization.
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Kinsel, Gary R., Kent Gillig, Ricky Edmondson, and David H. Russell. "Fundamental Investigations of the Mechanism of Laser Desorption and Ionization in Matrix Assisted Laser Desorption / Ionization." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.thb.1.

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The recent development of Matrix Assisted Laser Desorption / Ionization (MALDI) has sparked a revolution in the field of high molecular weight mass spectrometry.1 Time-of-flight (TOF) mass spectra of proteins weighing up to 300,000 Da are now routinely produced and this achievement has fostered a variety of bioanalytical applications which were previously unapproachable using conventional mass spectrometric techniques. These successful applications have burgeoned in spite of a poor understanding of the mechanism of analyte desorption and ionization under MALDI conditions. An improved understanding of the MALDI mechanism should aid in overcoming a number of limitations of the current state-of-the-art and forms the motivation for the work described.
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Scott, C. T. J., C. Kosmidis, W. J. Jia, K. W. D. Ledingham, and R. P. Singhal. "Investigations of desorbed species from matrix materials used in MALDI." In The 7th international symposium: Resonance ionization spectroscopy 1994. AIP, 1995. http://dx.doi.org/10.1063/1.47635.

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Drake, Wonder, Erin Seeley, and Richard Caprioli. "Matrix-Assisted Laser Desorption/Ionization (MALDI) Imaging Mass Spectrometry (IMS) Localize Mycobacterial Proteins To Sarcoidosis Granulomas." In American Thoracic Society 2010 International Conference, May 14-19, 2010 • New Orleans. American Thoracic Society, 2010. http://dx.doi.org/10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a3984.

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Hafenstine, Glenn. "Matrix-assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry for Advanced Polymer Charaterization." In 46th Polymeric Materials, Adhesives, and Composites (PolyMAC) Conference; KCNSC; June 21-23, 2022; KCNSC. US DOE, 2022. http://dx.doi.org/10.2172/1872439.

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Kobylis, Paulina, Hanna Lis, Piotr Stepnowski, and Magda Caban. "Verification of the homogeneity of the matrix/analyte mixture on sample plate using MALDI-MS technique and new ionic liquid matrices." In Człowiek Nauka Środowisko. Institute of Biotechnology and Molecular Medicine Foundation, 2018. http://dx.doi.org/10.31708/spi3.18/pkoby.cns18.

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Shah, Neeraj, Rebecca Gorton, Jennifer Canizales, Gina Birch, Timothy McHugh, and Marc Lipman. "The value of rapid speciation of nontuberculous mycobacteria (NTM) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF)." In Annual Congress 2015. European Respiratory Society, 2015. http://dx.doi.org/10.1183/13993003.congress-2015.pa370.

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Lee, Adam Michael, Jessica Moertel, Kangsheng Wang, and Robert B. Diasio. "Abstract 5451: High-throughput detection of dihydropyrimidine dehydrogenase gene (DPYD) variants using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF)." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-5451.

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Khaliullin, T., E. R. Sekera, A. B. Hummon, M. Rojas, and A. L. Mora. "Spatially-Resolved Lipidomic Analysis of Normal and Idiopathic Pulmonary Fibrosis (IPF) Human Lungs Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI)." In American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC. American Thoracic Society, 2023. http://dx.doi.org/10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2284.

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Peixoto, Paulo Henrique Soares, FERNANDO VICTOR MONTEIRO PORTELA, BRUNO NASCIMENTO DA SILVA, MARIA LAÍNA SILVA, and ROSSANA DE AGUIAR CORDEIRO. "PERFIL CLÍNICO-EPIDEMIOLÓGICO DE INFECÇÕES PELO COMPLEXO CANDIDA PARAPSILOSIS EM UM HOSPITAL PEDIÁTRICO TERCIÁRIO." In II Congresso Nacional de Microbiologia Clínica On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/ii-conamic/38.

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Introdução: As espécies de Candida estão associadas a diversos tipos de manifestações clínicas e são as principais responsáveis por infecções fúngicas em hospitais terciários. São conhecidas 200 espécies do gênero, dentre essas, destaca-se o Complexo C. parapsilosis, formado pelas espécies C. parapsilosis sensu stricto, C. orthopsilosis e C. metapsilosis, indistinguíveis nos laboratórios de microbiologia clínica. Objetivo: O presente projeto tem como objetivo conhecer o perfil clínico-epidemiológico das infecções de sítios profundos causadas pelo Complexo C. parapsilosis em população pediátrica atendida no Hospital Infantil Albert Sabin (HIAS). Material e métodos: A pesquisa foi aprovada pelo Comité de Ética do hospital em questão (Nº do parecer 4.207.133). Será realizado um estudo prospectivo em um período de 18 meses, iniciado em 11 de agosto de 2020, compreendendo duas etapas: A primeira consiste na triagem das amostras por meio da identificação das espécies em sistema automatizado Vitek® (C. parapsilosis e/ou Candida spp.), isoladas a partir de espécimes clínicos encaminhados ao Laboratório de Análises Clínicas no Setor de Microbiologia do HIAS. A posteriori os isolados serão confirmados com a técnica de Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Na segunda etapa, será realizada a coleta de dados dos pacientes de interesse, por meio da análise de prontuários médicos. Resultados: Transcorridos 12 meses do início da pesquisa, 3.514 exames foram positivos para pesquisa de bactérias e fungos e, deste total, 3.066 foram exames de sítios profundos. Até o momento, 101 amostras foram selecionadas para o estudo. 91 amostras foram identificadas como C. parapsilosis e 10 como Candida spp. Foi detectado resistência ao fluconazol em 1 isolados do Complexo C. parapsilosis e 2 isolados de Candida spp., a micafungina 1 isolado do Complexo C. parapsilosis e a fluocitosina 1 isolados de Candida spp. Conclusão: Do total de amostras de interesse, 89 (88,11%) foram de sangue, deste, 59 (58,41%) foram oriundas do Centro Pediátrico do Câncer. O conhecimento da distribuição do patógeno possibilitará ganhos futuros nas abordagens de prevenção e tratamento.
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Reports on the topic "MALDI matrix"

1

Puretzky, A. A., and D. B. Geohegan. LIF-imaging and gas-phase diagnostics of laser desorbed MALDI-matrix plumes. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/563317.

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Korte, Andrew R. Development of matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) for plant metabolite analysis. Office of Scientific and Technical Information (OSTI), December 2014. http://dx.doi.org/10.2172/1226566.

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Thurlow, James. 2018 Social Accounting Matrix for Mali: A Nexus Project SAM. Washington, DC: International Food Policy Research Institute, 2021. http://dx.doi.org/10.2499/p15738coll2.134818.

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Fluhr, Robert, and Maor Bar-Peled. Novel Lectin Controls Wound-responses in Arabidopsis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697123.bard.

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Innate immune responses in animals and plants involve receptors that recognize microbe-associated molecules. In plants, one set of this defense system is characterized by large families of TIR–nucleotide binding site–leucine-rich repeat (TIR-NBS-LRR) resistance genes. The direct interaction between plant proteins harboring the TIR domain with proteins that transmit and facilitate a signaling pathway has yet to be shown. The Arabidopsis genome encodes TIR-domain containing genes that lack NBS and LRR whose functions are unknown. Here we investigated the functional role of such protein, TLW1 (TIR LECTIN WOUNDRESPONSIVE1). The TLW1 gene encodes a protein with two domains: a TIR domain linked to a lectin-containing domain. Our specific aim in this proposal was to examine the ramifications of the TL1-glycan interaction by; A) The functional characterization of TL1 activity in the context of plant wound response and B) Examine the hypothesis that wounding induced specific polysaccharides and examine them as candidates for TL-1 interactive glycan compounds. The Weizmann group showed TLW1 transcripts are rapidly induced by wounding in a JA-independent pathway and T-DNA-tagged tlw1 mutants that lack TLW1 transcripts, fail to initiate the full systemic wound response. Transcriptome methodology analysis was set up and transcriptome analyses indicates a two-fold reduced level of JA-responsive but not JA-independent transcripts. The TIR domain of TLW1 was found to interact directly with the KAT2/PED1 gene product responsible for the final b-oxidation steps in peroxisomal-basedJA biosynthesis. To identify potential binding target(s) of TL1 in plant wound response, the CCRC group first expressed recombinant TL1 in bacterial cells and optimized conditions for the protein expression. TL1 was most highly expressed in ArcticExpress cell line. Different types of extraction buffers and extraction methods were used to prepare plant extracts for TL1 binding assay. Optimized condition for glycan labeling was determined, and 2-aminobenzamide was used to label plant extracts. Sensitivity of MALDI and LC-MS using standard glycans. THAP (2,4,6- Trihydroxyacetophenone) showed minimal background peaks at positive mode of MALDI, however, it was insensitive with a minimum detection level of 100 ng. Using LC-MS, sensitivity was highly increased enough to detect 30 pmol concentration. However, patterns of total glycans displayed no significant difference between different extraction conditions when samples were separated with Dionex ICS-2000 ion chromatography system. Transgenic plants over-expressing lectin domains were generated to obtain active lectin domain in plant cells. Insertion of the overexpression construct into the plant genome was confirmed by antibiotic selection and genomic DNA PCR. However, RT-PCR analysis was not able to detect increased level of the transcripts. Binding ability of azelaic acid to recombinant TL1. Azelaic acid was detected in GST-TL1 elution fraction, however, DHB matrix has the same mass in background signals, which needs to be further tested on other matrices. The major findings showed the importance of TLW1 in regulating wound response. The findings demonstrate completely novel and unexpected TIR domain interactions and reveal a control nexus and mechanism that contributes to the propagation of wound responses in Arabidopsis. The implications are to our understanding of the function of TIR domains and to the notion that early molecular events occur systemically within minutes of a plant sustaining a wound. A WEB site (http://genome.weizmann.ac.il/hormonometer/) was set up that enables scientists to interact with a collated plant hormone database.
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