Ultraflex 2 maldi tof tof

Manufactured by Bruker

Sourced in Germany, United States

The Ultraflex II MALDI-TOF/TOF is a high-performance mass spectrometry instrument manufactured by Bruker. It is designed for versatile and sensitive analysis of a wide range of samples, including proteins, peptides, oligonucleotides, and small molecules. The instrument combines Matrix-Assisted Laser Desorption/Ionization (MALDI) with Time-of-Flight (TOF) mass analyzers and tandem MS/MS capabilities for detailed structural characterization.

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18 protocols using ultraflex 2 maldi tof tof

Peptide Purification and MALDI-TOF-TOF Mass Spectrometry

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Example 8

Synthetic peptides were purified by C18 ZipTips™ (Millipore) before mass spectrometry analysis, as follows: 10 μl of 70% acetonitrile (ACN)/0.1% triflouroacetic acid (TFA) was pipetted two times through the ZipTip to wet the resin, followed by two 10 μl washes of 0.1% TFA to equilibrate the resin. The acidified peptide sample was aspirated up and down five times through the ZipTip to bind peptides to the resin. Contaminants were washed by pipetting 0.1% TFA three times through the ZipTip before eluting the bound peptides into a fresh tube using 70% ACN/0.1% TFA. The peptides were dried in a speed vac, re-suspended in 10 μl 0.1% TFA before mixing with matrix (α-cyano-4 hydroxycinnamic acid or sinapinic acid) at a ratio of 1:4 before analysis. Mass spectrometry was performed using a Bruker Daltonics Ultraflex II™ MALDI-TOF-TOF and the data acquired in both the reflectron and linear positive modes.

US10414799B2. Peptide compounds to regulate the complement system (2019-09-17). ReAlta Holdings, LLC [US]. Inventors: Neel K. Krishna [US], Kenji Cunnion [US].

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Quantitative Peptidomic Analysis via MALDI-TOF-MS

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS)-based rapid quantitative peptidomic analysis was performed using the BLOTCHIP-MS method (Protosera, Amagasaki, Japan) as described previously [27 (link),28 (link)]. Samples (25 μl) of GCF or rat GEC supernatant were mixed with 30 μl of NuPAGE LDS sample buffer (Life Technologies, Carlsbad, CA, USA). After a brief centrifugation, the supernatants were transferred to new tubes, heated for 10 min at 70°C, and then chilled on ice. A sample (25 μl) was processed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) using NuPAGE Novex 4–12% Bis-Tris Mini Gels (Life Technologies). After electrophoresis, the slab gel was cut into strips and placed on chips. Then, peptides in the gel were electroblotted onto pre-wetted BLOTCHIP using an XCell II Blot Module (Life Technologies). The MALDI matrix, CHCA (Sigma-Aldrich, St. Louis, MO, USA), was applied onto the BLOTCHIP using an automatic matrix-dispensing machine (Protosera). All MS spectra were acquired on an UltraFlex II MALDI-TOF/TOF (Bruker Daltonics, Billerica, MA, USA) under previously defined conditions [28 (link)]. Each sample was measured in quadruplicate.

Tancharoen S., Matsuyama T., Kawahara K.I., Tanaka K., Lee L.J., Machigashira M., Noguchi K., Ito T., Imamura T., Potempa J., Kikuchi K, & Maruyama I. (2015). Cleavage of Host Cytokeratin-6 by Lysine-Specific Gingipain Induces Gingival Inflammation in Periodontitis Patients. PLoS ONE, 10(2), e0117775.

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Peptide Purification and MALDI-TOF-TOF Analysis

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Example 8

US09914753B2. Peptide compounds to regulate the complement system (2018-03-13). Eastern Virginia Medical School [US], Children's Health Foundation, Inc. [US], Eriko Life Sciences Ventures, LLC [US]. Inventors: Neel K. Krishna [US], Kenji Cunnion [US].

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Purification and Characterization of HO-1 Protein Complexes

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Recombinant GSTHO-1 protein complexes were pull-downed with Glutathione-S-agarose coated beads and the pull-down fractions with the co-precipitated proteins were washed and loaded onto SDS-PAGE gels and stained with Colloidal Coomasie. The bands were excised, and proteins were reduced using dithiothreitol (DTT), alkylated with iodoacetamide and digested with trypsin. For MALDI-TOF/TOF analyses, peptides were desalted and concentrated in a C18 resin (Zip-Tips. Waters Coorporation). MS and MSMS spectra were acquired using Ultraflex II MALDI TOF/TOF (Bruker Daltonics). Database analysis: MALDI MS and MSMS spectra were analyzed using Flex Analysis and Biotools Software (Bruker Daltonics). The peaklists obtained were processed and compared with NCBI databases using Protein Prospector and/or Mascot Software. Searches were performed against the human genome, allowing a peptide tolerance of 200 ppm, and a fragment tolerance of 0.7 Da.To control for nonspecific binding, we compared HO-1GST-extracted proteins to those pulled down with GST. Only differential HO-1GST-binding proteins compared to GST-binding proteins were considered further.

Gueron G., Giudice J., Valacco P., Paez A., Elguero B., Toscani M., Jaworski F., Leskow F.C., Cotignola J., Marti M., Binaghi M., Navone N, & Vazquez E. (2014). Heme-oxygenase-1 implications in cell morphology and the adhesive behavior of prostate cancer cells. Oncotarget, 5(12), 4087-4102.

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MALDI-TOF Lipid Imaging in Tissue

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DHB matrix (50 mg/mL) dissolved in 6:4 (v/v) MeOH/0.1% TFA in water was manually sprayed at a flow rate of 300 μL/h using a syringe pump connected to an electrospray nebulizer. The nebulizer was connected to a nitrogen line operated at 1 bar. The nebulizer was moved uniformly throughout the tissue until crystallization was sufficient to ensure optimal lipid detection. The tissue was then analyzed using an UltraFlex II MALDI-TOF/TOF (Time Of Flight) mass spectrometer equipped with a Smartbeam Nd-YAG laser (355 nm) and controlled by FlexControl software (Bruker Daltonics, Bremen, Germany). Lipid image acquisition was performed in positive reflector mode within an m/z range of 50 to 900 at a 300 μm resolution, and the obtained spectra were averaged from 300 laser shots per pixel. Peak detection and spatial segmentation analysis were then performed on the acquired images using SCiLS Software 2015b (SCiLS Lab GmbH, Bremen, Germany). For spatial segmentation, the Bisecting k-Means approach with Correlation as the distance metric was used. Spectra were subjected to median normalization and medium denoising prior to peak picking. After analysis, the ROIs were determined by selecting segments where the correlation distance metric is significantly distant from the other.

Delcourt V., Franck J., Leblanc E., Narducci F., Robin Y.M., Gimeno J.P., Quanico J., Wisztorski M., Kobeissy F., Jacques J.F., Roucou X., Salzet M, & Fournier I. (2017). Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine, 21, 55-64.

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MALDI-TOF/TOF Mass Spectrometry Analysis

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Mass spectra were acquired under linear and reflectron modes, using a Bruker Ultraflex II MALDI-TOF/ TOF controlled by FLEXCONTROL 3.0 software (Bruker Daltonics, Bremen, Germany). External calibration was performed while using Peptide Standard Calibration II (Bruker Daltonics) and Peptide Calibration Mix 3 (PepMix3; New England Biolabs, Ipswich, MA, USA) for reflection and linear modes, respectively. The matrix, α-cyano-4-hydroxycinnamic acid (Sigma-Aldrich, St. Louis, MO, USA) was prepared at a concentration of 20 mg·mL⁻¹ in 1:1 acetonitrile containing 0.1% TFA solution. AbeTx1 solution (1μL) dropped onto the MALDI sample plate (384 positions; Bruker Daltonics) was added to the matrix solution (1μL) and dried at room temperature. Spectra were analyzed using thebFLEXANALYSIS 3.0 program (Bruker Daltonics Software).

B. Orts D.J., Peigneur S., Silva-Gonçalves L.C., Arcisio-Miranda M., P. W. Bicudo J.E, & Tytgat J. (2018). AbeTx1 Is a Novel Sea Anemone Toxin with a Dual Mechanism of Action on Shaker-Type K+ Channels Activation. Marine Drugs, 16(10), 360.

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Enzymatic Digestion of AbeTx1

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AbeTx1 sample was digested with Endopeptidase LysC (Sigma-Aldrich) at 37 °C for 30, 60, and 120 min, in an enzyme:toxin ratio of 1:10, 1:20 and 1:100 (w/w) in Tris-HCl (150 mM, pH 8.5). Molecular weights of enzymatic fragments were acquired, as described before, using a Bruker Ultraflex II MALDI-TOF/TOF (Bruker Daltonics).

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MALDI-TOF/TOF Analysis of Biomolecules

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The droplets containing captured materials were collected and analyzed by MALDI MS. Each captured droplet was directly mixed onto the MALDI plate with 1 μL of matrix solution. Appropriated matrix and standard protocols were used according to the family of analyzed biomolecules i.e. HCCA (10 mg; ACN/TFA 0.1%aq, 7:3, v/v) for peptides, SA (20 mg; ACN/TFA 0.1%aq, 6:4, v/v) for proteins and 2,5-DHB (30 mg; MeOH/TFA 0.1%aq, 1:1, v/v) for lipids. Samples were subsequently analyzed on an Ultraflex II MALDI-TOF/TOF (Bruker Daltonics, GmBH, Bremen, Germany) mass spectrometer equipped with a Smart Beam Laser (modified Nd:YAG, λ = 355 nm) in positive reflectron and linear modes. For each sample, MS spectra were recorded from the accumulation of 2000 laser shots at a repetition rate of 100Hz. Mass spectra were processed with FlexAnalysis 3.2 software (Bruker Daltonics GmBH, Bremen, Germany).

Fatou B., Wisztorski M., Focsa C., Salzet M., Ziskind M, & Fournier I. (2015). Substrate-Mediated Laser Ablation under Ambient Conditions for Spatially-Resolved Tissue Proteomics. Scientific Reports, 5, 18135.

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MALDI-TOF MS Protocol for Microalgae and Cyanobacteria

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Mass spectrometry was done using an UltraFlex II MALDI-TOF TOF (Bruker Daltonics GmbH, Leipzig, Germany) mass spectrometer with fuzzy control of laser intensity. Ion source 1 was set at 25 kV and ion source 2 was set at 23.5 kV with a laser frequency of 50.0 Hz, a detector gain of 1,650 V, and a gating maximum of 1,500 Da. Spectra were recorded in the positive linear mode for the mass range of 2,000 to 20,000 m/z. Each spectrum was obtained by averaging 600 laser shots acquired in the automatic mode. For data acquisition and validation measurements were performed in Auto Execute mode. The spectra were externally calibrated using the Bacterial Test Standard (Bruker Daltonics). The standard consisted of seven ribosomal proteins from Escherichia coli with added RNase A and myoglobin to cover a range of ca. 3637 to 16957 m/z (Da).
Four independent samples of each microalgae and cyanobacteria isolate were placed on four separate spots on a ground steel MALDI target plate (see supplementary Figure 3). Each sample spot was read twice thereby producing eight spectra per isolate. The quality and mass accuracy of the peaks were examined using the FlexAnalysis software (Bruker Daltonics). The eight spectra were overlaid and a consensus spectrum generated which was added to the database for each isolate.

Emami K., Hack E., Nelson A., Brain C.M., Lyne F.M., Mesbahi E., Day J.G, & Caldwell G.S. (2015). Proteomic-based biotyping reveals hidden diversity within a microalgae culture collection: An example using Dunaliella. Scientific Reports, 5, 10036.

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Peptide-Proteoliposome Interaction Analysis

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VIP and CRF were purchased from Sigma Genosys (Japan). The remaining synthetic peptides were obtained from Peptides Institute (Osaka, Japan). Reconstituted peptides (10 pmol each), either alone or in combination, were incubated with 0.5 mg of proteoliposomes for 1 h at 25 °C. The reaction mixture was extensively washed to eliminate unbound peptides by repeated ultracentrifugation at 10,000 × g and resuspension of the pellet with 10 mM Tris-HCl (pH 7.4). Peptides specifically bound to the proteoliposomes were eluted with 0.3 N HCl containing 0.1% Triton X-100. The molecular masses of the peptides in the eluates were determined using a ProteinChip Reader PBSIIc (Ciphergen Biosystems) or a BLOTCHIP (Protosera, Kobe, Japan), a target plate for MALDI-MS^{39 (link)}, and subsequent analysis with an Ultra-flex II MALDI-TOF/TOF (Bruker Daltonics).

Shichiri M., Nonaka D., Lee L.J, & Tanaka K. (2018). Identification of the salusin-β receptor using proteoliposomes embedded with endogenous membrane proteins. Scientific Reports, 8, 17865.

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