Maldi ms software

Manufactured by Shimadzu

Sourced in United Kingdom

MALDI-MS software is a data analysis tool for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) instrumentation. It provides core functions for processing and analyzing MALDI-MS data.

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Axima performance, by Shimadzu (1 mentions) Axima performance maldi tof tof mass spectrometer, by Shimadzu (1 mentions) Axima confidence maldi tof ms, by Shimadzu (1 mentions)

6 protocols using maldi ms software

MALDI-TOF Characterization of DNA Oligonucleotides

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Either
a biotinylated 31-, 83-, or 84-mer DNA sequence (100 pmol) was mixed
with 2 μL of matrix containing 1 μL of 3-hydroxy picolinic
acid (3-HPA) (50 mg/mL dissolved in acetonitrile/water 50% v/v) and
1 μL of diammonium hydrogen citrate (DAHC) (50 mg/mL dissolved
in acetonitrile/water 50% v/v). MALDI-TOF experiments were performed
using Axima Performance from Shimadzu Biotech. The mass spectrometric
measurement of 31-mer oligonucleotides was carried out in a reflectron
positive mode. The calibration of the instrument in reflectron positive
mode was performed using low-molecular-weight oligonucleotide or peptide
standard calibration kit. For high-molecular-weight oligonucleotides
(>10 000 Da), calibration was done in a linear negative
mode
using 52-, 80-, 90-, and 100-mer standards with laser power 120 in
order to enhance the signal intensity. The spectral data was processed
by using Shimadzu Biotech MALDI-MS software with processing parameters
as follows: smoothing filter width as 20 channels, baseline filter
width as 80 channels, and double threshold.

Xu L., Vaidyanathan V.G, & Cho B.P. (2014). Real-Time Surface Plasmon Resonance Study of Biomolecular Interactions between Polymerase and Bulky Mutagenic DNA Lesions. Chemical Research in Toxicology, 27(10), 1796-1807.

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MALDI-TOF MS Analysis of Eravacycline Metabolism

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The matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis was performed as previously reported (33 (link)), with minor modifications. In brief, 100 mM N-Tris(hydroxymethyl) methylaminopropane sulfonic acid (TAPS) (pH 7.5), 500 μM NADPH, 50 μM eravacycline, 0.5 mM MgCl₂, and 1.25 μM enzyme was adjusted to a final volume of 100 μl in an Eppendorf tube. The tube was then mixed and incubated in a metal bath at 37°C for 15 min. After incubation, a 1:3 mixture of hydrochloric acid and acetonitrile was added to stop the reaction. Subsequently, 1 μl supernatant was spotted onto an MSP 384 target polished steel plate (Shimadzu, Kyoto, Japan) and left to dry at room temperature, and then 1 μl matrix (α-cyano-4-hydroxycinnamic acid) was taken to cover the target point. A Shimadzu Performance mass spectrometer and Shimadzu Biotech MALDI-MS software were used to acquire mass spectra in positive linear ion mode operating between 100 and 1,000 Da.

Cui C.Y., He Q., Jia Q.L., Li C., Chen C., Wu X.T., Zhang X.J., Lin Z.Y., Zheng Z.J., Liao X.P., Kreiswirth B.N., Liu Y.H., Chen L, & Sun J. (2021). Evolutionary Trajectory of the Tet(X) Family: Critical Residue Changes towards High-Level Tigecycline Resistance. mSystems, 6(3), e00050-21.

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MALDI-TOF Analysis of Polymers

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An AXIMA performance instrument was used in reflection mode with Dithranol as the matrix. A thin layer of a NaI solution (1 μL, 0.01 mmol/mL in THF) was first deposited on the target plate, followed by the solutions of the matrix (2 μL, 10 mg/mL in CHCl₃) and polymer (2 μL, 5 mg/mL in THF) were mixed. The mixed solution was spotted on the MALDI sample plate and air-dried. The raw data was processed in the Shimadzu Biotech MALDI-MS software.

Tu Y.M., Gong F.L., Wu Y.C., Cai Z, & Zhu J.B. (2023). Insights into substitution strategy towards thermodynamic and property regulation of chemically recyclable polymers. Nature Communications, 14, 3198.

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MALDI-TOF Analysis of Limousin Oak Extract

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MALDI-TOF spectra were recorded using a Kratos compact MALDI Axima Performance TOF 2 instrument (Shimadzu Biotech, Manchester, UK), equipped with a nitrogen laser (337 nm), an ion gate for the selection of precursor ions, and a collision cell, according to Lagel et al. (2014) . The windows for separation of precursor ions were approximately 4 Da. Argon has been used as the collision gas. All data were obtained in positive ion linear mode applying the accumulation of 441 scans per spectrum. Linear negative mode was used for the investigation of hydrolysable and glycosylated molecular patterns which characterise the Limousin oak extract. The calibration of the linear modes was done using phosphorus red pigment as a reference over a mass range up to 2500 Da. NaCl was added in the sampling wells as the salt to enhance ion formation previous deposition of samples. The MALDI-TOF target was then analysed to give the resulting spectra, using a raster analysis over the target; Maldi-MS software was used for data treatment (Shimadzu Biotech, Manchester, UK).

Ricci A., Parpinello G.P., Palma A.S., Teslić N., Brilli C., Pizzi A, & Versari A. (2017). Analytical profiling of food-grade extracts from grape (Vitis vinifera sp.) seeds and skins, green tea (Camellia sinensis) leaves and Limousin oak (Quercus robur) heartwood using MALDI-TOF-MS, ICP-MS and spectrophotometric methods. Journal of food composition and analysis : an official publication of the United Nations University, International Network of Food Data Systems, 59.

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Mass Spectrometry Analysis of E. coli rRNA

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E. coli expressing empty plasmid or Cfr were grown at 37°C to an OD₆₀₀ of 0.4–0.6 with shaking by diluting an overnight culture 1:100 into LB media containing ampicillin (100 µg/ml) and AHT inducer (30 ng/ml). Total RNA purification, oligo-protection of the 23S rRNA fragment C2480-C2520, and RNaseT1 digestion were performed as described previously (Stojković and Fujimori, 2015 (link); Andersen et al., 2004 (link)). Mass spectra were acquired in positive ion, reflectron mode on an AXIMA Performance MALDI TOF/TOF Mass Spectrometer (Shimadzu). Relative peak intensity values were calculated using the Shimadzu Biotech MALDI-MS software.

Tsai K., Stojković V., Noda-Garcia L., Young I.D., Myasnikov A.G., Kleinman J., Palla A., Floor S.N., Frost A., Fraser J.S., Tawfik D.S, & Fujimori D.G. (2022). Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. eLife, 11, e70017.

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MALDI-TOF MS Analysis of Lipid A

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Purified lipid A samples were dissolved in a small amount (30–100 μL) of 2:1 chloroform/methanol. A sample of this solution was mixed in situ on a MALDI target slide with 20 mg/mL 6-aza-2-thiothymine in 9:9:2 water/acetonitrile/10% ammonium citrate in ratios ranging from 4:1 to 1:4, with a maximum total load volume of 2 μL. Spectral data were collected by Shimadzu Axima Confidence MALDI-TOF MS in the negative or positive linear mode (pulsed extraction 2000 Da) as the average of up to 2000 shots at moderate power (see individual figure legends for details). Shimadzu MALDI-MS software was used to perform the following processing of the raw data: (1) Calibration of all spectra to mode-specific standard datasets built from spectral data for wild-type E. coli hexa-acyl bis-phosphate lipid A (Figure 1) and E. coli tetra-acyl bis-phosphate (data not shown); (2) Averaging of all profiles collected for each sample; (3) Processing with a baseline filter width of 100 channels, threshold-apex peak detection, and an averaged peak smoothing width of 30–100 channels to resolve molecular weights from the clusters of individual isotopic masses.

Sweet C.R., Alpuche G.M., Landis C.A, & Sandman B.C. (2014). Endotoxin Structures in the Psychrophiles Psychromonas marina and Psychrobacter cryohalolentis Contain Distinctive Acyl Features. Marine Drugs, 12(7), 4126-4147.

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