Data analysis 3

Manufactured by Bruker

Sourced in Germany, United States

Data Analysis 3.4 is a software platform developed by Bruker for the analysis and interpretation of scientific data. It provides a comprehensive set of tools for data visualization, processing, and statistical analysis.

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Lab products found in correlation

Microtof q type qq tof ms instrument, by Bruker (5 mentions) Biotools 3, by Bruker (3 mentions) Ultimate 3000, by Thermo Fisher Scientific (2 mentions) Mascot, by Matrix Science (2 mentions) Cosmosil 5c18 ms 2 column, by Nacalai Tesque (2 mentions) Mascot 2, by Matrix Science (2 mentions) Reflex 3 maldi tof ms, by Bruker (1 mentions) Waters 2996 photodiode array detector pda, by Waters Corporation (1 mentions) Europa protein 300 c8, by Teknokroma (1 mentions) 2695 separations module, by Waters Corporation (1 mentions) Amx 500 spectrometer, by Bruker (1 mentions) Tunemix mixture, by Bruker (1 mentions) Microtof q instrument, by Bruker (1 mentions) Vario el cube, by Elementar (1 mentions) Silica gel 60, by Merck Group (1 mentions) Kieselgel 60 f254, by Merck Group (1 mentions) Avance 2 500 spectrometer, by Bruker (1 mentions) Agilent 1200 series lc system, by Agilent Technologies (1 mentions) Zorbax sb c18 column, by Agilent Technologies (1 mentions) Maxis ultra high resolution q tof mass spectrometer, by Bruker (1 mentions)

Close spelling variants of this product

Data Analysis software version 3.4 (6 citations) Daltonics Data Analysis 3.4 Mass Spectrometer (3 citations) Data Analysis software (Version 4.3). (2 citations)

38 protocols using data analysis 3

High-Resolution FTICR-MS Analysis of Humic Substances

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FTICR MS analysis
of the HS samples was performed using an FT MS spectrometer Bruker
Apex Ultra (Bruker Daltonics) equipped with a dynamically harmonized
cell, a 7 T superconducting magnet, and an electrospray ionization
(ESI) source. Each of the mass spectra were acquired in negative ionization
mode by direct infusion at a flow rate of 120 mL·h^–1 by summarizing 400 scans. The internal calibration of the obtained
mass spectra was systematically conducted using the known peak series
of HS, reaching accuracy values of <0.5 ppm. Mass lists were created
using Data Analysis 3.4 software (Bruker Daltonics). Molecular assignments
were made using lab-made Transhumus software. Ion charge was directly
determined for abundant peaks using the m/z difference between ¹³C and ¹²C isotopologues,
and was extended for minor peaks using the total mass differences
algorithm.^{45 (link)} Formulae were filtered using
the following typical atomic constraints: O/C ≤ 1, H/C ≤
2.2, C ≤ 120, H ≤ 200, 0 < O ≤ 60, and N ≤
2, S ≤ 1.

Mikhnevich T.A., Vyatkina (Turkova) A.V., Grigorenko V.G., Rubtsova M.Y., Rukhovich G.D., Letarova M.A., Kravtsova D.S., Vladimirov S.A., Orlov A.A., Nikolaev E.N., Zherebker A, & Perminova I.V. (2021). Inhibition of Class A β-Lactamase (TEM-1) by Narrow Fractions of Humic Substances. ACS Omega, 6(37), 23873-23883.

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MALDI-TOF-MS and nanoLC-FT ICR MS Analysis

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MALDI-TOF MS was performed on a Bruker Reflex III MALDI-TOF-MS (Bruker Daltonics, Germany) operating in the reflectron mode with 20 kV accelerating voltage and 23 kV Reflecting voltage [25 (link)]. A saturated solution of cyano-4-hydroxy-cinnamic acid in 50% acetonitrile and 0.1% trifluoroactic acid was used as the matrix. Sample preparation for the mass spectrometry followed the protocol reported by Geng and colleagues [25 (link)]. One μL the matrix solution and one μL sample solution were added in the Score 384 target well. The mass spectrometry analysis was performed by a specialist in the Instrument Application Center of the Academy of Military Medical Sciences following the previously published protocol [25 (link)]. In brief, mass accuracy for peptide mass finger-prints (PMF) analysis was calibrated with a 0.1–0.2 Da external standard, and internal calibration was carried out with enzyme autolysis peaks, at a resolution of 12,000. The nanoLC- FT ICR MS was performed on an APEX-Q FT-ICR tandem mass spectrometer (Bruker Daltonics, Germany) equipped with a 9.4 T superconducting magnet (Magnex Scientific, UK) and an infinity cell. The trypsin digested peptides were sequenced by auto MS mode with MS/MS boost function. The FT-ICR mass spectra were processed using Data Analysis 3.4 software (Bruker Daltonics GmbH, Germany) as a gateway to set up database searches.

Xu G., Tang X., Shang X., Li Y., Wang J., Yue J, & Li Y. (2018). Identification of immunogenic outer membrane proteins and evaluation of their protective efficacy against Stenotrophomonas maltophilia. BMC Infectious Diseases, 18, 347.

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Copper(II)-induced Oxidation Reaction Analysis

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HPLC-MS measurements were used to identify the products of the copper(II)-induced oxidation reactions and were performed by a MicroTOF-Q type Qq-TOF MS instrument (Bruker Daltonik, Bremen, Germany) operated in positive ion mode and a Waters 2695 Separations Module with a Teknokroma Europa Protein 300 C8 (250 × 4.6 mm, 300 Å, 5 μm), a thermostable autosampler (5 °C), a column module (35 °C) and a Waters 2996 Photodiode-array detector (PDA). The MS instrument was equipped with an electrospray ion source, where the spray voltage was 4 kV. N₂ was utilized as a drying gas; the drying temperature was 200 °C, and the flow rate was 9.0 L/min. The same HPLC method was used as described above. The mass spectra were calibrated externally using the exact masses of clusters [(NaTFA)_n⁺Na]⁺ generated from the electrosprayed solution of sodium trifluoroacetate (NaTFA). The spectra were evaluated with the DataAnalysis 3.4 software from Bruker. The analytes were detected with a PDA detector at λ = 222 nm, while the flow rate and the injection volume were 1.0 mL/min and 10 μL, respectively.

Kastal Z., Balabán A., Vida S., Kállay C., Nagy L., Várnagy K, & Sóvágó I. (2024). Copper(II), Nickel(II) and Zinc(II) Complexes of Peptide Fragments of Tau Protein. Molecules, 29(10), 2171.

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Profiling Bioactive Phenolics in Ficus via LC-MS

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The bioactive phenolic compounds were profiled by LC–MS using the mass analyzer Bruker micrOTOF-Q, Bruker, Germany. A reverse phase C18 column (Phenomenex 250 mm, 5 μm particle size) was used. The eluting system consisted of water acidified with 0.1% formic acid and (1:1, v/v) acetonitrile/methanol acidified with 0.1% formic acid as solvent A and B respectively. The 0.45 μm membrane disk filter was used to filter the mobile phase and degassed by sonication before injection. The parameters which were used to the Elution process are as follows: 5% B, 0–5 min; 5%–10% B, 5–10 min; 10%–50% B, 10–55 min; 50%–95% B, 55–65 min; 5% B, 65–70 min. The 20 μL of solvent was injected with 0.4 mL/min flow rate. The analytical parameters with negative ion mode were performed as follows: source temperature 150 °C, desolvation temperature 350 °C, cone voltage 50 eV, capillary voltage 3 kV, cone gas flow 50 L/h, desolvation gas flow 600 L/h. The ion mass spectra were acquired between m/z 50–1000 and the peaks data were processed using the Bruker Daltonics Data Analysis 3.4 software. By comparing with the retention time of spectra and reported mass spectrum data with the literature on genus Ficus and family Moraceae, the bioactive compounds were identified.

Shahinuzzaman M., Akhtar P., Amin N., Ahmed Y., Anuar F.H., Misran H, & Akhtaruzzaman M. (2021). New insights of phenolic compounds from optimized fruit extract of Ficus auriculata. Scientific Reports, 11, 12503.

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Deuterated Standard Materials Characterization

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The characterization of the deuterated standard materials was performed by liquid chromatograph—mass spectrometry measurements. For chromatography, a Waters 2695 Separations Module (Waters, Milford, MA, USA) equipped with a thermostable autosampler (5 °C) and a column module (40 °C), a Waters 2996 photodiode-array detector and a VDSphere PUR 100 C18-M-SE (4.6 × 150 cm, 5 µm) column. Gradient elution was used with 1.5 mL/min flow rate. Mobile phase A was ACN (acetonitrile) containing 0.02% formic acid and mobile phase B was water containing 0.02% formic acid. The gradient condition was as follows: initially 20% A and 80% B, 0–20 min linear change to 50% A and 50% B, 20–30 min linear change to 90% A and 10% B and held this setting for additional 10 min. The analytes were detected at λ = 240 nm. Mass spectrometric detection was carried out by a MicroTOF-Q type Qq-TOF MS instrument (Bruker Daltoniks) using an ESI-source with negative ion mode. The spray voltage was set to 4.5 kV. The nebulizer pressure was 1.6 bar, while, the temperature of the drying gas (N₂, 7 L/min) was kept at 200 °C. The data evaluation was performed by the DataAnalysis 3.4 software from Bruker.

Nagy T., Róth G., Kuki Á., Zsuga M, & Kéki S. (2021). Mass Spectral Filtering by Mass-Remainder Analysis (MARA) at High Resolution and Its Application to Metabolite Profiling of Flavonoids. International Journal of Molecular Sciences, 22(2), 864.

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CHNS, ESI-MS, and NMR Characterization

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CHNS elemental analysis was carried out by a Vario EL cube (Elementar, Germany) calibrated on acetanilide. Electrospray ionization mass spectroscopy (ESI-MS) (micrOTOF-Q instrument; Bruker Daltonics, Germany) allowed for the MS spectra to be obtained. The ESI-MS instrument was operated in the positive ion mode and calibrated with the Tunemix^TM mixture (Bruker Daltonics, Germany). The mass accuracy was better than 5 ppm. The obtained mass spectra were analyzed using DataAnalysis 3.4 software (Bruker Daltonics, Germany). ¹H NMR spectra were recorded on a Bruker AMX-500 spectrometer, using CDCl₃ as a solvent. ¹H chemical shifts (in ppm) were calibrated to TMS as an internal reference. Melting points were determined using a Boetius melting point apparatus, while Krafft temperatures were determined according to the directions given in [47 (link)]. CMC is the minimum concentration above which micelles are formed in aqueous liquid. To obtain the CMC values, we used McGowan’s model. This method shows the relationship between partition coefficients and molecular volumes. Molecular characteristic volumes (V_x) are found by the addition of the atomic characteristic volumes and the subtraction for the same factory (6.56 × 10⁻⁶ m³ mol⁻¹) for every covalent bond.

Paluch E., Bortkiewicz O., Widelski J., Duda-Madej A., Gleńsk M., Nawrot U., Lamch Ł., Długowska D., Sobieszczańska B, & Wilk K.A. (2024). A Combination of β-Aescin and Newly Synthesized Alkylamidobetaines as Modern Components Eradicating the Biofilms of Multidrug-Resistant Clinical Strains of Candida glabrata. International Journal of Molecular Sciences, 25(5), 2541.

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DART-MS Characterization of Samples

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The DART-MS measurements were carried out with a MicroTOF-Q type Qq-TOF MS instrument (Buker Daltoniks, Bremen, Germany), equipped by the DART SVP ion source (Ionsense, Inc., Saugus, MA, USA). All spectra were recorded by a digitizer at a sampling of 2 GHz. The spectra were evaluated by the DataAnalysis 3.4 software from Bruker.
The ion source temperature was 350 °C, He (5.0) was applied for the ionization. The samples were inserted manually to the source.

Pardi-Tóth V., Kuki Á., Kordován M.Á., Róth G., Nagy L., Zsuga M., Nagy T, & Kéki S. (2023). Molecular data storage using direct analysis in real time (DART) ionization mass spectrometry for decoding. Scientific Reports, 13, 16576.

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Analytical Characterization of CBD Extract

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CBD was purchased from https://www.cbdepot.eu (Prague, Czech Republic). Kieselgel 60 F254 (Merck, Darmstadt, Germany) sheets were used for thin-layer chromatography. Detection was performed by immersing into ammonium molybdate-sulfuric acid solution and heating. Silica gel 60 (Merck, Darmstadt, Germany, 0.040–0.063 mm) was used for Flash column chromatography. Bruker Avance II 500 spectrometer (Bruker, Germany) was used for recording the ¹H NMR (500 MHz), ¹³C NMR (125 MHz), and 2D spectra. Me₄Si (0.00 ppm for ¹H) and solvent residual signals were used as reference for chemical shifts. (NMR spectra can be found in the Supporting Information.) ESI-TOF MS spectra were recorded by a microTOF-Q type QqTOFMSmass spectrometer (Bruker, Germany). It was used in negative or positive ion mode. MeOH was the solvent, and calibration of the mass spectra was performed using the exact masses of clusters [(NaTFA)_n + TFA]⁺ from the solution of sodium trifluoroacetate (NaTFA). DataAnalysis 3.4 software from Bruker was used for the evaluation of the spectra.

Szőke K., Kajtár R., Gyöngyösi A., Czompa A., Fésüs A., Lőrincz E.B., Petróczi F.D., Herczegh P., Bak I., Borbás A., Bereczki I, & Lekli I. (2023). Pharmacological Evaluation of Newly Synthesized Cannabidiol Derivates on H9c2 Cells. Antioxidants, 12(9), 1714.

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Tandem Mass Spectrometry Analysis

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A MicroTOF-Q type Qq-TOF MS instrument (Bruker Daltonik, Bremen, Germany) was used for the MS/MS measurements. The instrument was equipped with an electrospray ion source where the spray voltage was 4 kV. N 2 was utilized as drying gas. The drying temperature was 180 °C and the flow rate was 4.0 L/min. For the MS/MS experiments, nitrogen was used as the collision gas and the collision energies were varied in the range of 1-39 eV (in the laboratory frame). The pressure in the collision cell was determined to be 1.2×10 -2 mbar. The precursor ions for MS/MS were selected with an isolation width of 4 m/z units. The mass spectra were recorded by means of a digitizer at a sampling rate of 2 GHz. The spectra were evaluated with the DataAnalysis 3.4 software from Bruker.

Nagy T., Kuki Á., Antal B., Nagy L., Purgel M., Sipos A., Nagy M., Zsuga M, & Kéki S. (2015). Chiral differentiation of the noscapine and hydrastine stereoisomers by electrospray ionization tandem mass spectrometry. Journal of mass spectrometry : JMS, 50(1).

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Mass Spectrometry Analysis Protocol

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A MicroTOF-Q type Qq-TOF MS instrument (Bruker Daltonik, Bremen, Germany) was used for the MS and MS/MS measurements in positive ion mode. The instrument was equipped with an electrospray ion source where the spray voltage was 4 kV. N 2 was utilized as drying gas. The drying temperature was 200 °C and the flow rate was 4.0 L/min (8.0 L/min HPLC-MS) using the same method described in 2.6. For the MS/MS experiments, nitrogen was used as the collision gas. The pressure in the collision cell was determined to be 1.2×10 -2 mbar.
The precursor ions for MS/MS were selected with an isolation width of 5 m/z units. The mass spectra were recorded by means of a digitizer at a sampling rate of 2 GHz. The mass spectra were calibrated externally using the exact masses of clusters [(NaTFA) n +Na] + generated from the electrosprayed solution of sodium trifluoroacetate (NaTFA). The spectra were evaluated with the DataAnalysis 3.4 software from Bruker. The sample solutions were introduced either directly into the ESI source with a syringe pump (Cole-Parmer Ins. Co., Vernon Hills, IL, USA) at a flow rate of 3 μL/min.

Csire G., Nagy L., Várnagy K, & Kállay C. (2017). Copper(II) interaction with the Human Prion 103-112 fragment - Coordination and oxidation. Journal of inorganic biochemistry, 170.

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