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Ltq ftms

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The LTQ-FTMS is a high-performance mass spectrometer that combines a linear ion trap (LTQ) with a Fourier transform ion cyclotron resonance (FTMS) analyzer. It provides high mass accuracy, high resolution, and sensitive detection for a wide range of analytical applications.

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Lab products found in correlation

Acquity uplc, by Thermo Fisher Scientific (2 mentions) Carrageenan, by Merck Group (1 mentions) Whatman no 1 sheets, by Cytiva (1 mentions) Hr esi ms, by Thermo Fisher Scientific (1 mentions) V 630, by Jasco (1 mentions) Ltq ft mass spectrometer, by Thermo Fisher Scientific (1 mentions) Trypsin, by Promega (1 mentions) Mascot search engine, by Matrix Science (1 mentions) L rhamnose, by Merck Group (1 mentions)

11 protocols using ltq ftms

1

Metabolomic Profiling Using UPLC-MS

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Extracts were split into two aliquots, dried, then reconstituted in acidic or basic LC-compatible solvents, each of which contained 11 or more injection standards at fixed concentrations. A Waters ACQUITY UPLC and a Thermo-Finnigan LTQ-FT MS were utilized for the analysis. One aliquot was analyzed using acidic positive ion optimized conditions and the other using basic negative ion optimized conditions in two independent injections using separate dedicated columns. Extracts reconstituted in acidic conditions were gradient eluted from a Waters BEH C18 2.1 x 100 mm, 1.7 μm column using water and methanol both containing 0.1% formic acid, while basic extracts, which also used water/methanol, contained 6.5 mM ammonium bicarbonate. MS analysis alternated between MS and data-dependent MS2 scans using dynamic exclusion, scanning from 80–1000 m/z. Accurate mass measurements were made on precursor ions with greater than 2 million counts; typical mass error was less than 5 ppm.
Jonscher K.R., Alfonso-Garcia A., Suhalim J.L., Orlicky D.J., Potma E.O., Ferguson V.L., Bouxsein M.L., Bateman T.A., Stodieck L.S., Levi M., Friedman J.E., Gridley D.S, & Pecaut M.J. (2016). Spaceflight Activates Lipotoxic Pathways in Mouse Liver. PLoS ONE, 11(4), e0152877.
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2

LC-MS/MS Fragmentation Profiling

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The LC/MS part of the platform consists of a Waters ACQUITY UPLC and a Thermo-Finnigan LTQ-FT MS. Fragmentation spectra (MS/MS) were obtained in a data-dependent manner. If needed, targeted MS/MS was used.
Lucarelli G., Ferro M., Loizzo D., Bianchi C., Terracciano D., Cantiello F., Bell L.N., Battaglia S., Porta C., Gernone A., Perego R.A., Maiorano E., de Cobelli O., Castellano G., Vincenti L., Ditonno P, & Battaglia M. (2020). Integration of Lipidomics and Transcriptomics Reveals Reprogramming of the Lipid Metabolism and Composition in Clear Cell Renal Cell Carcinoma. Metabolites, 10(12), 509.
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3

Quantification of Lung Adenocarcinoma CD26/DPP4 Activity

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We have previously provided data on the activity of CD26/DPP4 from patients bearing lung adenocarcinoma including the methodology how to obtain these activities (23) . In brief, we analyzed thirty-eight pairs of fresh-frozen human lung adenocarcinoma biopsies and corresponding normal lung tissues from patients who underwent surgical resection at the University Hospital Zurich between 2003 and 2006 (TNM stage: IA to IV). Proteins were labelled with the fluorophosphates derivative 6-Nbiotinylaminohexyl isopropyl phosphorofluoridate (FP-1) serving as an activity probe. Labelled proteins enriched with streptavidin-beads were digested with trypsin and analyzed on an FT-ICR mass spectrometer (LTQ-FTMS, Thermo Finnigan). Tandem mass spectrometry data were searched in the recently updated human database (UniProtKB/Swiss-Prot) with Mascot 2.2 search engine. For relative quantification, MS data were analyzed with Progenesis LC-MS version 2.5 (Nonlinear Dynamics) with the three most intense peptides matching to a protein by The median ratio of the top three intense peptide ions matching to enzymes in malignant versus normal tissues was used. The specific activity of CD26/DPP4 was presented as the relative activity of mean activity of normal tissue.
A c c e p t e d M a n u s c r i p t 6
Jang J.H., Janker F., De Meester I., Arni S., Borgeaud N., Yamada Y., Gil Bazo I., Weder W, & Jungraithmayr W. (2019). The CD26/DPP4-inhibitor vildagliptin suppresses lung cancer growth via macrophage-mediated NK cell activity. Carcinogenesis, 40(2).
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4

Phytochemical Characterization of Compounds

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The NMR spectra were run at 300 and 500 (1H), 75 and 125 (13C) MHz, on Varian Mercury 300 and JEOL GX-500 NMR spectrometers, respectively. The chemical shifts (δ) are reported in ppm downfield to TMS in the appropriate deuterated solvent. For ESI-MS analyses, LCQ (Finnigan MAT 95, Bremen, Germany) and LTQ-FT-MS spectrometers were used, while HR-ESI-MS (Thermo Electron, Finnigan, Germany) was used for HR-ESI-MS analyses. UV spectrophotometer (JASCO V-630) was used for analysis of pure samples in MeOH and in different UV shift reagents.
Material for column chromatography (CC), including microcrystalline cellulose, polyamide S 6 and Sephadex LH-20, as well as Whatman No. 1 sheets used for paper chromatography were purchased from sources described in our previous literature.[11 (link)] Isolated compounds were detected using Naturstoff[11 (link)] and/or FeCl3 (1% in ethanol) spray reagents. Solvent systems S1 (n-BuOH/HOAc/H2O; 4:1:5 v/v/v top layer), S2 (HOAc/H2O; 15:85 v/v) and S3 (n-BuOH/iso-propanol/H2O; 4:1:5, v/v/v top layer) were used. Indomethacin was obtained from Epico, Egypt; paracetamol and silymarin from Sedico, 6th October, Egypt; carrageenan from Sigma, USA; alanine aminotransferase (ALT), alkaline phosphatase (ALP) and aspartate aminotransferase (AST) kits were purchased from Marcy’ Étoile (France).
Moharram F.A., El Dib R.A., Marzouk M.S., El-Shenawy S.M, & Ibrahim H.A. (2017). New Apigenin Glycoside, Polyphenolic Constituents, Anti-inflammatory and Hepatoprotective Activities of Gaillardia grandiflora and Gaillardia pulchella Aerial Parts. Pharmacognosy Magazine, 13(Suppl 2), S244-S249.
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5

Peptide Extraction and LC-MS/MS Analysis

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Gel spots were destained and subjected to trypsin (20 ng/μL; Promega) digest. Further extraction of peptides from the gel material was performed twice, and these solutions were collected and combined. The supernatant solutions of extracted peptides were combined and dried in a vacuum centrifuge. The samples were then subjected to liquid chromatography (LC)–tandem mass spectrometry (MS/MS) analysis by the HSC Core at the University of Utah. Specifically, peptides were analyzed using a nano–LC-MS/MS system comprised of a nano-LC pump (Eksigent, AB SCIEX, Framingham, MA) and an LTQ-FT mass spectrometer (Thermo Electron Corporation, Waltham, MA). LTQ-FT MS raw data files were processed to peak lists with BioWorks Browser 3.2 software (Thermo Electron Corporation). Resulting DTA files from each data acquisition file were merged, and the data file was searched for identified proteins against the National Center for Biotechnology Information (NCBI) database, mouse taxonomy subdatabase, using Mascot search engine (version 2.2.1; Matrix Science). Identified peptides were accepted only when the Mascot ion score value exceeded 20.
Wende A.R., Schell J.C., Ha C.M., Pepin M.E., Khalimonchuk O., Schwertz H., Pereira R.O., Brahma M.K., Tuinei J., Contreras-Ferrat A., Wang L., Andrizzi C.A., Olsen C.D., Bradley W.E., Dell’Italia L.J., Dillmann W.H., Litwin S.E, & Abel E.D. (2020). Maintaining Myocardial Glucose Utilization in Diabetic Cardiomyopathy Accelerates Mitochondrial Dysfunction. Diabetes, 69(10), 2094-2111.
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6

Spectroscopic Analysis of Organic Compounds

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The NMR spectra were recorded using Bruker a 400 MHz for 1 H NMR and 100.40 MHz for 13 C NMR. The spectra were run in DMSO, and chemical shifts were given as δ ppm relative to tetramethylsilane (TMS) as an internal standard. Negative ESI-MS were run on LCQ deca MS and LTQ-FT-MS spectrometers for MS analysis (Thermo Electron, Finnigan, Germany). For column chromatography, silica gel G60 for column chromatography (70-230 mesh, Merk), silica gel G60 for thin layer chromatography (E. Merk, Germany), silica gel GF254 pre-coated TLC plates (E. Merk, Germany), sheets of Whatman filter paper (1 mm) for paper Chromatography (WhatmanItd, Maid stone, Kent, England), micro crystalline cellulose (E. Merk-Darmstadt, Germany) and polyamide 6S (Riedel-De-Haen AG, SeelzeHaen AG, SeelzeHanver, Germany). Solvent systems for paper chromatography: S1 (n-BuOH-HOAc-H2O 4: 1: 5, top layer), S2 (15% aqueous HOAc) were used [7] .
Ibrahim H.A., ELSHARAWY F.S., Hassab M.A.E., Shabana S., & Haggag E. (2020). PHYTOCHEMICAL SCREENING AND BIOLOGICAL EVALUATION OF DYPSIS LEPTOCHEILOS LEAVES EXTRACT AND MOLECULAR DOCKING STUDY OF THE ISOLATED COMPOUNDS. International Journal of Pharmacy and Pharmaceutical Sciences.
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7

Synthesis and Characterization of Carbohydrate Derivatives

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All reactions were performed using dry solvents in flame-dried glassware under a nitrogen atmosphere with magnetic stirring, unless otherwise noted. Reaction solvents were dried over 4 Å molecular sieves, according to a published procedure (Bradley et al., 2010 (link)). EA was purchased from Sigma-Aldrich and stored in a vacuum desiccator over DrieriteTM and phosphorous pentoxide. Phenol and catechol were obtained from Spectrum Chemical (New Brunswick, NJ, USA) and TCI American (Portland, OR, USA). L-rhamnose was purchased from Sigma-Aldrich; D-mannose and D-xylose were obtained from Chem-Impex International Inc. (Wood Dale, IL, USA). All commercially sourced chemicals and reagents were used as received. Thin layer chromatography (TLC) was performed on alumina plates coated with silica gel 60 F254 and visualized under UV light or by staining with basic KMnO4 solution. Silica gel 60 (40–63 μm) was used for flash column chromatography. 1H and 13C NMR (nuclear magnetic resonance) spectra were recorded on UNITY Plus 600, INOVA 400, and Mercury 300 spectrometers. Chemical shifts are reported in ppm and referenced to the residual solvent signal (for 1H NMR: CDCl3 = 7.26 ppm, CD3OD = 3.31 ppm, DMSO-d6 = 2.50 ppm; for 13C NMR: CDCl3 = 77.16 ppm, CD3OD = 49.00 ppm, DMSO-d6 = 39.52 ppm). High-resolution mass spectra were obtained using a Thermo LTQ FTMS.
Fontaine B.M., Nelson K., Lyles J.T., Jariwala P.B., García-Rodriguez J.M., Quave C.L, & Weinert E.E. (2017). Identification of Ellagic Acid Rhamnoside as a Bioactive Component of a Complex Botanical Extract with Anti-biofilm Activity. Frontiers in Microbiology, 8, 496.
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8

Synthesis of Fluorinated Silyl Ether Compound

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Compound 13b was prepared from 12b using the same procedure as for compound 13a; yield 39%. 1H NMR (400 MHz, CDCl3) δ 7.94 – 7.86 (m, 4H), 7.64 – 7.53 (m, 6H), 4.31 – 4.17 (m, 4H), 3.66 (d, J = 6.6 Hz, 1H), 1.30 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 135.59, 132.06, 130.15, 127.95, 118.26 (t, J = 30.3 Hz), 115.73 (t, J = 30.3 Hz), 114.38 (t, J = 32.6 Hz), 113.19 (t, J = 30.1 Hz), 111.77 (t, J = 32.7 Hz), 109.17 (t, J = 32.6 Hz), 61.78 (t, J = 26.8 Hz), 60.70 (t, J = 25.1 Hz), 26.50, 19.32. 19F NMR (377 MHz, CDCl3) δ −122.34 (p, J = 12.0. Hz)p), −124.07 (p, J = 14.3 Hz), 126.81 MS (Thermo LTQ-FTMS): m/z [M+Na]+ calcd. for C21H24F6NaO2Si: 473.1342, found: 473.1341.
Mahmoud S., Li H., McBrayer T.R., Bassit L., Hammad S.F., Coats S.J., Amblard F, & Schinazi R.F. (2016). Synthesis and antiviral evaluation of fluorinated acyclo-nucleosides and their phosphoramidates. Nucleosides, nucleotides & nucleic acids, 36(1), 66-82.
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9

Trifluoromethanesulfonylation of Phenol Derivative

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To a solution of compound 13a (0.60 mmol, 240 mg) in dry CH2Cl2 (1 mL) at −20°C were added pyridine (1.70 mmol, 0.1 mL, 2.8 eq.) and Tf2O (0.7 mmol, 0.1 mL, 1.15 eq.). The mixture was stirred for 2 hours at −20°C and quenched with 5% HCl (3 mL). The organic layer was separated and washed with 5% HCl (5 mL), H2O (5 mL) and brine (5 mL), dried over sodium sulfate and concentrated under reduced pressure to afford compound 14a (0.54 mmol, 287 mg, 90%) as a yellow oil. 1H NMR (400 MHz, CDCl3) δ 8.00 – 7.88 (m, 4H), 7.68 – 7.55 (m, 6H), 5.20 (t, J = 13.8 Hz, 2H), 4.29 – 4.19 (m, 2H), 1.33 (s, 9H). 13C NMR (101 MHz, CDCl3) δ 135.66, 131.48, 130.55, 128.26, 123.51, 120.34, 118.43 (t, J = 29.8 Hz), 117.16, 116.55 – 115.41 (m), 114.31 – 113.23 (m), 70.13 (t, J = 24.4 Hz), 61.66 = (t, J = 30.0 Hz), 26.56, 19.24. 19F NMR (377 MHz, CDCl3) δ −75.75, −123.73 (t, J = 12.3 Hz), −123.91 (t, J = 14.0 Hz). MS (Thermo LTQ-FTMS): m/z [M+Cl]− calcd. for C21H23ClF7O4SSi: 567.0668, found: 567.0679.
Mahmoud S., Li H., McBrayer T.R., Bassit L., Hammad S.F., Coats S.J., Amblard F, & Schinazi R.F. (2016). Synthesis and antiviral evaluation of fluorinated acyclo-nucleosides and their phosphoramidates. Nucleosides, nucleotides & nucleic acids, 36(1), 66-82.
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10

TBDPS Protection of Alcohol Compound 12a

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To a solution of compound 12a (2.30 mmol, 372 mg) in dry CH2Cl2 (5 mL) at 0°C were added imidazole (4.70 mmol, 313 mg, 2 eq.) and TBDPSCl (2.30 mmol, 0.6 mL, 1 eq.). The mixture was stirred overnight and evaporated under reduced pressure. The residue was purified by silica gel column chromatography eluting with hexane:ethyl acetate (80:20) to afford compound 13a (0.92 mmol, 370 mg, 40%) as a yellow oil. 1H NMR (400 MHz, CDCl3) δ 7.90 – 7.81 (m, 4H), 7.55 (q, J = 7.3, 6.2 Hz, 6H), 4.19 (t, J = 14.4 Hz, 4H), 3.45 (s, 1H), 1.25 (s, 9H). 13C NMR (101 MHz, = CDCl3) δ 135.69, 131.95, 130.37, 128.13, 118.86 (td, J = 31.0, 9.3 Hz), 116.35 (td, J = 31.1, 9.7 Hz), 113.84 (td, J = 31.3, 10.2 Hz), 61.78 (t, J = 28.6 Hz), 60.67 (t, J = 26.0 Hz), 26.69, 19.36. 19F NMR (377 MHz, CDCl3) δ −124.23 (t, J = 13.3 Hz), −125.58 (t, J = 14.5 Hz). MS (Thermo LTQ-FTMS): m/z [M+Na]+ calcd. for C20H24F4NaO2Si: 423.1373, found: 423.1377.
Mahmoud S., Li H., McBrayer T.R., Bassit L., Hammad S.F., Coats S.J., Amblard F, & Schinazi R.F. (2016). Synthesis and antiviral evaluation of fluorinated acyclo-nucleosides and their phosphoramidates. Nucleosides, nucleotides & nucleic acids, 36(1), 66-82.
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