Foundation 3

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Thermo Fisher Scientific Foundation 3.1 is a versatile lab equipment designed for various applications. It features a compact and durable construction, with a focus on delivering reliable performance. The core function of this product is to provide a stable and controlled environment for various laboratory processes.

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Lab products found in correlation

Xcalibur 3, by Thermo Fisher Scientific (4 mentions) 5800 maldi tof tof analyzer, by AB Sciex (1 mentions) Xcalibur 4, by Thermo Fisher Scientific (1 mentions) Dataexplorer software 4, by AB Sciex (1 mentions)

5 protocols using foundation 3

Mass Spectrometry Data Analysis

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Obtained mass spectrometry data were handled using Xcalibur 3.1 with Foundation 3.1 (Thermo Fisher Scientific, USA). A signal-to-noise ratio (S/N) value of 100 was considered to detect m/z peaks, and exported peak lists were further processed using Microsoft Excel. Elemental formulas for the detected m/z peaks were assigned within typical conditions of C_cH_hN_nO_o, counting c unlimited, h unlimited, and 0 ≤ n ≤ 10, and 0 ≤ o ≤ 50 using MIDAS Formula Calculator. ChemDraw Professional 15.0 (PerkinElmer, Waltham, MA, USA) was used to draw the structures of the identified compounds. A Venn diagram for the overlapped peaks was generated by FunRich 3.1.3 [74 (link)].
Compound identification was executed by comparing theoretically calculated masses of [M–H]⁻ and [M+Cl]⁻ adducts with the observed m/z peak values. For the structural elucidation of the detected phytochemicals, ESI–MS/MS- and APCI–MS/MS-produced fragments of the target peaks were compared with the Human Metabolome Database (online database) [15 (link)] and literatures.

Islam S., Alam M.B., Ann H.J., Park J.H., Lee S.H, & Kim S. (2020). Metabolite Profiling of Manilkara zapota L. Leaves by High-Resolution Mass Spectrometry Coupled with ESI and APCI and In Vitro Antioxidant Activity, α-Glucosidase, and Elastase Inhibition Assays. International Journal of Molecular Sciences, 22(1), 132.

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Mass Spectrometry-Based Compound Identification

Cited 1 time

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Mass spectral data obtained from the orbitrap MS were processed using Xcalibur 3.1 with Foundation 3.1 (Thermo Fisher Scientific). Compounds were tentatively identified by matching their exact (calculated) masses of protonated (M + H) adducts with measured m/z values and PSI-MS/MS fragmentation patterns from the in-house MS/MS database, and online databases such as the Human Metabolome Database [15 (link)] and METLIN [16 (link)], and the literature. The compound structures were drawn using ChemDraw Professional 15.0 (PerkinElmer, Waltham, MA, USA).

Alam M.B., Ahmed A., Islam S., Choi H.J., Motin M.A., Kim S, & Lee S.H. (2020). Phytochemical Characterization of Dillenia indica L. Bark by Paper Spray Ionization-Mass Spectrometry and Evaluation of Its Antioxidant Potential Against t-BHP-Induced Oxidative Stress in RAW 264.7 Cells. Antioxidants, 9(11), 1099.

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MALDI-ToF/ToF Mass Spectrometry Analyses

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All experiments were
performed using a 5800 MALDI-ToF/ToF analyzer (AB SCIEX, Darmstadt,
Germany) equipped with a neodymium-doped yttrium lithium fluoride
(Nd:YLF) laser (345 nm), in a reflectron positive mode, with a typical
mass accuracy of 10 ppm. In MS and MS/MS modes, 1000 laser shots were
typically accumulated by a random rastering pattern, at laser pulse
rates of 400 and 1000 Hz, respectively; each shown mass spectrum was
averaged on at least five single mass spectra (1000 laser shots each).
The laser fluences were within 1.9–2.6 J/m² depending
on the matrix employed. MS/MS experiments were performed setting a
potential difference of 1 kV between the source and the collision
cell; ambient air was used as the collision gas with a medium pressure
of 10^–6 Torr. The delayed extraction time was set
at 280 ns.
DataExplorer software 4.0 (AB Sciex) was used to
control the acquisitions and to perform the initial elaboration of
data, whereas SigmaPlot 11.0 was used to graph the final mass spectra.
ChemDraw Pro 8.0.3 (CambridgeSoft Corporation, Cambridge, MA) was
employed to draw chemical structures. Isotopic pattern contribution
was generated by Xcalibur 4.0 with Foundation 3.1 (Thermo Fisher Scientific).

Calvano C.D., Capozzi M.A., Punzi A., Farinola G.M., Cataldi T.R, & Palmisano F. (2018). 1,5-Diaminonaphtalene is a Highly Performing Electron-Transfer Secondary-Reaction Matrix for Laser Desorption Ionization Mass Spectrometry of Indolenine-Based Croconaines. ACS Omega, 3(12), 17821-17827.

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Metabolite Identification Using Mass Spectrometry

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Mass spectrum data acquired from the orbitrap mass spectrometer were organized using Xcalibur 3.1 along with foundation 3.1 (Thermo Fisher Scientific Inc. Rockford, IL, USA). The m/z peaks were tentatively identified by matching their exact (theoretical) masses of deprotonated (M-H) adducts with measured m/z values and ESI-MS/MS fragmentation patterns from an in-house MS/MS database, and online databases such as FooDB (https://foodb.ca/, accessed date 2 April 2021) and METLIN database (https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage, accessed date 2 April 2021). Compound structures were drawn using ChemDraw Professional 15.0 (PerkinElmer, Waltham, MA, USA).

Alam M.B., Naznin M., Islam S., Alshammari F.H., Choi H.J., Song B.R., Kim S, & Lee S.H. (2021). High Resolution Mass Spectroscopy-Based Secondary Metabolite Profiling of Nymphaea nouchali (Burm. f) Stem Attenuates Oxidative Stress via Regulation of MAPK/Nrf2/HO-1/ROS Pathway. Antioxidants, 10(5), 719.

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Mass Spectrometry Data Analysis

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The mass spectral data was analyzed with Xcalibur 3.1 with Foundation 3.1 (Thermo Fisher Scientific, Rockford, IL, USA). The detected m/z peaks were identified by comparing the exact masses of monoisotopic (negative mode) masses and ESI-MS/MS breakage patterns from an online database and as in-house MS/MS database. The online databases included FooDB [31 (link)], METLIN [32 (link)], and CFM-ID 4.0 [33 (link)].

Javed A., Naznin M., Alam M.B., Fanar A., Song B.R., Kim S, & Lee S.H. (2022). Metabolite Profiling of Microwave-Assisted Sargassum fusiforme Extracts with Improved Antioxidant Activity Using Hybrid Response Surface Methodology and Artificial Neural Networking-Genetic Algorithm. Antioxidants, 11(11), 2246.

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