Autoflex 2 tof tof mass spectrometer

Manufactured by Bruker

Sourced in Germany

The Autoflex II TOF/TOF mass spectrometer is a high-performance instrument designed for matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and tandem time-of-flight (TOF/TOF) mass spectrometry. The core function of this product is to provide accurate and reliable mass analysis of a wide range of analytes, including proteins, peptides, and other biomolecules.

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Lab products found in correlation

Vacufuge plus, by Eppendorf (1 mentions) Clinpro tools software 3, by Bruker (1 mentions) Flexcontrol 2, by Bruker (1 mentions) Mascot, by Matrix Science (1 mentions) Sep pak plus c18 environmental cartridge, by Waters Corporation (1 mentions) Xbridge ost c18 2.5 μm, by Waters Corporation (1 mentions) Sep pak plus c18 cartridge, by Waters Corporation (1 mentions) Acquity uplc, by Waters Corporation (1 mentions) Q tof mass spectrometer, by Waters Corporation (1 mentions) Smz745t microscope, by Nikon (1 mentions) Flexanalysis 2, by Bruker (1 mentions) Acquity uplc system, by Waters Corporation (1 mentions)

Close spelling variants of this product

Autoflex II MALDI-TOF/TOF mass spectrometer Autoflex II MALDI-TOF mass spectrometer Autoflex TOF/TOF mass spectrometer Autoflex II ToF/ToF spectrometer Autoflex II mass spectrometer Autoflex mass spectrometer Autoflex II TOF/TOF Autoflex II spectrometer Autoflex II Bruker spectrometers

7 protocols using autoflex 2 tof tof mass spectrometer

Proteomic Analysis of Sheep Proteins

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The protein spots were carefully excised from gels and then de-stained for 30 min in wash buffer (100 μL, 25 mM NH₄HCO₃/50% acetonitrile (v/v)). Washed-out gel-spots (dehydrated in 100% acetonitrile) were dried completely with a centrifuge (Vacufuge plus, Eppendorf, Hamburg, Germany) and then incubated in 15 ng/μL trypsin and 25 mM NH₄HCO₃ (37 °C, 16 h). The peptides were incubated in trifluoroacetic acid (20 μL, 0.1% (v/v), 37 °C, 40 min) after digestion. The above extraction procedures were repeated by using 50% acetonitrile/0.1% trifluoroacetic acid (v/v). Sediments were washed in trifluoroacetic acid and then vacuum freeze-dried for further analysis. The proteins were identified by using AUTOFLEX II TOF-TOF mass spectrometer (autoflex™ speed, Bruker Daltonik, Bremen, Germany). Samples in 1 μL of buffer (50% acetonitrile and 5 mg/mL α-CHCA in 0.1% trifluoroacetic acid) were loaded on plate (AnchorChip, 384-MPT).
Each crystallized sample was washed by using 0.1% trifluoroacetic acid for removing salt ions. Protein identification was performed by peptide mass fingerprinting (PMF), searching the Mascot (2.2 version, Matrix Science, London, UK), and matched with a sheep (Ovis aries) family in the Uniprot database (https://www.uniprot.org/ (accessed on 8 October 2021)), correspondingly.

Gao X., Zhao D., Wang L., Cui Y., Wang S., Lv M., Zang F, & Dai R. (2021). Proteomic Changes in Sarcoplasmic and Myofibrillar Proteins Associated with Color Stability of Ovine Muscle during Post-Mortem Storage. Foods, 10(12), 2989.

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MALDI-TOF MS protocol for protein identification

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The AnchorChip target plate was placed in an Autoflex II TOF/TOF mass spectrometer (Bruker Daltonics) controlled by Flexcontrol 2.4 software (Bruker Daltonics). The instrument has a 337 nm nitrogen laser, delayed‐extraction electronics, and a 25 Hz digitizer and was externally calibrated using standard procedures. All acquisitions were obtained in LIFT mode using an automated acquisition method included in the instrument software and based on averaging 1000 randomized shots. The acquisition laser power was set between 20 and 35%. Spectra were acquired in positive linear mode in the mass range 600–10 000 Da. Peak clusters were completed using the second pass peak section (signal to noise ratio >5).
The relative peak intensities (normalized to a total ion current of between 1000 and 10 000 m/z) were expressed as arbitrary units. All measurements were performed using ClinProTools software 3.0 (Bruker Daltonics).
Five hundred laser shots from a total of 3000 laser shots were summed. The averaged MALDI‐MS/MS spectrum was subjected to a database search via the Mascot (Matrix Science, UK) database search engine using the search parameters: no enzyme specificity, 25 ppm mass tolerance for the parent mass, and 0.2 Da for the fragment masses. No fixed or variable modifications were selected. The NCBInr database was used for the search.

Tsuchida S., Satoh M., Umemura H., Sogawa K., Takiwaki M., Ishige T., Miyabayashi Y., Iwasawa Y., Kobayashi S., Beppu M., Nishimura M., Kodera Y., Matsushita K, & Nomura F. (2018). Assessment by Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry of the Effects of Preanalytical Variables on Serum Peptidome Profiles Following Long‐Term Sample Storage. Proteomics. Clinical Applications, 12(3), 1700047.

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Synthesis and Purification of BnAEO-Modified ODNs

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Syntheses of the ODNs containing B^AEO was performed on an automated DNA synthesizer (Gene Design, nS‐8) at the 0.2 μmol scale. Activator 42® was used as the activator. The coupling time of the standard phosphoramidite coupling protocol was increased from 30 s to 12 min. The B^AEO phosphoramidite 9 was prepared with 0.10 m acetonitrile/THF (v/v, 3:1). The ON synthesis was performed in the DMTr‐on mode. CPG‐supported ODNs were cleaved and the protecting groups of the nucleobases were removed with 50 mm K₂CO₃ in MeOH at RT for 4 h. The DMTr group in ODNs were detritylated and purified with a Sep‐Pak^® Plus C18 Cartridge and Sep‐Pak® Plus C18 Environmental Cartridge (Waters) [washed with 10 % acetonitrile aqueous solution, detritylated with 0.5 % aqueous trifluoroacetic acid solution, and eluted with 35 % aqueous MeOH solution]. ODNs were purified by means of reverse‐phase HPLC on a Waters XBridge^TM OST C18 2.5 μm (10×50 mm) with 0.1 m triethylammonium acetate buffer (pH 7.0) (buffer a) and acetonitrile (buffer b). The purified ODNs were analyzed by means of reverse‐phase HPLC on a Waters XBridge^TM OST C18 2.5 μm (4.6×50 mm) column. The structures of ODNs were determined by means of MALDI‐TOF MS (Bruker Daltonics AutoflexII TOF/TOF mass spectrometer).

Kishimoto Y., Nakagawa O., Fujii A., Yoshioka K., Nagata T., Yokota T., Hari Y, & Obika S. (2020). 2′,4′‐BNA/LNA with 9‐(2‐Aminoethoxy)‐1,3‐diaza‐2‐oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance. Chemistry (Weinheim an Der Bergstrasse, Germany), 27(7), 2427-2438.

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Determining Chelator Moieties in Antibodies

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Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry was performed to determine the average number of chelator moieties per Ab molecule. The matrix was a 2,5-dihydroxyacetophenone (DHAP)-based solution consisting of 7.6 mg 2,5-DHAP for MALDI-MS (Merck) in 375 μL absolute ethanol with 125 μL of an 18 mg/mL aqueous solution of diammonium hydrogen citrate. The sample was mixed with 2% trifluoroacetic acid and matrix solution at equal volumes and pipetted up and down until crystallization started. Then, 0.5 µL crystalized sample was added on the steel ground target and allowed to dry. Measurements were carried out with an Autoflex II TOF/TOF mass spectrometer (Bruker, Billerica, MA, USA) and analyses of the spectra with flexAnalysis software 3.4.

Striese F., Neuber C., Gräßel S., Arndt C., Ullrich M., Steinbach J., Pietzsch J., Bergmann R., Pietzsch H.J., Sihver W., Frenz M., Feldmann A, & Bachmann M.P. (2023). Preclinical Characterization of the 177Lu-Labeled Prostate Stem Cell Antigen (PSCA)-Specific Monoclonal Antibody 7F5. International Journal of Molecular Sciences, 24(11), 9420.

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Peptoid Characterization by LC-MS and MALDI-TOF

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Peptoids were characterised by accurate LC-MS (QToF mass spectrometer and an Acquity UPLC from Waters Ltd) using an Acquity UPLC BEH C8 1.7 μm (2.1 mm × 50 mm) column with a flow rate of 0.6 ml min^–1 and a linear gradient of 5–95% of solvent B over 3.8 min (A = 0.1% formic acid in H₂O, B = 0.1% formic acid in MeCN). Peptide identities were also confirmed by MALDI-TOF mass spectra analysis (Autoflex II ToF/ToF mass spectrometer Bruker Daltonik GmBH) operating in positive ion mode using an α-cyano-4-hydroxycinnamic acid (CHCA) matrix. Data processing was done with MestReNova version 8.1.
Analytical RP-HPLC was carried out using a Perkin Elmer Series 200 lc pump fitted with a series 200 UV/vis detector and autosampler using a SB-Analytical ODH-S optimal column (100 × 1.6 mm, 3.5 μm); flow rate 1 ml min^–1; λ = 220 nm, linear gradient elution 0–100% of solvent B over 30 min (A = 0.05% TFA, 95% H₂O, 5% MeCN, B = 0.03% TFA, 5% H₂O, 95% MeCN).

Bolt H.L., Eggimann G.A., Jahoda C.A., Zuckermann R.N., Sharples G.J, & Cobb S.L. (2017). Exploring the links between peptoid antibacterial activity and toxicity †The authors declare no competing interests. ‡Electronic supplementary information (ESI) available. See DOI: 10.1039/c6md00648e. MedChemComm, 8(5), 886-896.

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Proteomic Profiling of Tumor Tissues

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Microdissections of neoplastic and healthy tissues were used for the identification of proteins. Microdissection was performed manually under a Nikon SMZ 745T microscope (Nikon, Budapest, Hungary). Dissected tissue samples were homogenized and separated by one-dimensional SDS-polyacrylamide gel electrophoresis. The spots of interest were excised from the gel with a medical scalpel, and then transported into new Eppendorf tubes. After destaining, the proteins were alkylated, reduced and subjected to an overnight tryptic digestion. The resulting peptides were purified and concentrated with solid phase extraction, and then spotted onto a MALDI target plate. The peptide mass fingerprint-based proteomics identification was performed by an Autoflex II TOF/TOF mass spectrometer (Bruker Daltonics, Bremen, Germany).

Schmidt J., Kajtár B., Juhász K., Péter M., Járai T., Burián A., Kereskai L., Gerlinger I., Tornóczki T., Balogh G., Vígh L., Márk L, & Balogi Z. (2020). Lipid and protein tumor markers for head and neck squamous cell carcinoma identified by imaging mass spectrometry. Oncotarget, 11(28), 2702-2717.

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Analytical LCMS and MALDI-TOF MS Analysis

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Analytical LCMS was carried out using an Acquity UPLC system (Waters Ltd, UK) equipped with a photodiode array detector. Samples were injected onto an Acquity UPLC BEH C18 column (1.7 μm, 2.1 × 50 mm) and a gradient of 5-95% B (solvent A = H 2 O, 0.1% formic acid; B = MeCN) was run over 3.8 min with a flow rate of 0.6 mL min -1 . The flow of solvent from the UPLC system was introduced into the electrospray ion source of an Aquity TQD or QToF Premier mass spectrometer, and positive ions were measured.
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) MALDI-TOF mass data was collected using an Autoflex II ToF/ ToF mass spectrometer (Bruker Daltonik GmBH) equipped with a 337 nm nitrogen laser. Peptides were dissolved in 1 : 1 deionized water/MeCN for MS analysis. Sample solution (1 mg mL -1 ) was mixed with matrix solution (α-cyano-4-hydroxycinnamic acid, ∼50 mg mL -1 ) in a ratio of 1 : 9, and 1 μL of the resulting solution spotted onto a metal target and placed into the MALDI ion source. MS data was processed using FlexAnalysis 2.0 (Bruker Daltonik GmBH). MALDI MS/MS was performed using LIFT technology, which enables detection of product ions that result from elevating the laser power.

Lear S., Munshi T., Hudson A.S., Hatton C., Clardy J., Mosely J.A., Bull T.J., Sit C.S, & Cobb S.L. (2016). Total chemical synthesis of lassomycin and lassomycin-amide. Organic & biomolecular chemistry, 14(19).

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