Ltq orbitrap discovery hybrid ftms

Manufactured by Thermo Fisher Scientific

Sourced in United States

The LTQ Orbitrap Discovery Hybrid FTMS is a high-performance mass spectrometry instrument designed for advanced research applications. It combines a linear ion trap (LTQ) with an Orbitrap mass analyzer, providing high mass accuracy, resolution, and sensitivity for the analysis of complex samples.

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Lab products found in correlation

Nanoacquity uplc, by Waters Corporation (4 mentions) Riboprobe system, by Promega (1 mentions) Proteome discoverer 1.4 interface, by Thermo Fisher Scientific (1 mentions) Mascot search engine, by Matrix Science (1 mentions) Nanoacquity hplc system, by Waters Corporation (1 mentions) Ltq orbitrap, by Thermo Fisher Scientific (1 mentions) Symmetry c18, by Waters Corporation (1 mentions)

5 protocols using ltq orbitrap discovery hybrid ftms

Identification of IRES-Binding Proteins

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Biotinylated RNAs containing full length (FL) IRES only (IRES), or 5’UTR sequences without IRES (ΔIRES) sequences were in vitro transcribed (Riboprobe systems, Promega) and used in pull-down assays. The differentially stained bands were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS). The Mass Spec data were uploaded to ProteomeXchange (http://www.proteomexchange.org/) under the accession number of PXD012892.
In parallel, the protein tryptic digests were fractionated using a nano-UPLC system (nanoACQUITY UPLC, Waters, Milford, MA) coupled to an ion trap mass spectrometer (LTQ Orbitrap Discovery Hybrid FTMS, Thermo Fisher Scientific) equipped with an electrospray ionization source. The raw data were searched against the NCBI-nr database (18132328 sequences, 6219145704 residues) using the Mascot search engine (Matrix Science) with the Proteome Discoverer 1.4 interface (Thermo Fisher Scientific).

Chen T.M., Lai M.C., Li Y.H., Chan Y.L., Wu C.H., Wang Y.M., Chien C.W., Huang S.Y., Sun H.S, & Tsai S.J. (2019). hnRNPM induces translation switch under hypoxia to promote colon cancer development. EBioMedicine, 41, 299-309.

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Peptide Fractionation and Tandem Mass Spectrometry

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The protein tryptic digests were fractionated using a flow rate of 400 nL/min with a nano-UPLC system (nanoACQUITY UPLC, Waters, Milford, MA, USA) coupled to an ion trap mass spectrometer (LTQ Orbitrap Discovery Hybrid FTMS, Thermo, San Jose, CA, USA) equipped with an electrospray ionization source. For reverse phase nano-UPLC-ESI-MS/MS analyses, a sample (2 μL) of the desired peptide digest was loaded into the trapping column (Symmetry C18, 5 μm, 180 μm × 20 mm) by an autosampler. Reverse phase separation was performed using a linear acetonitrile gradient from 99% buffer A (100% D.I. water/0.1% formic acid) to 85% buffer B (100% acetonitrile/0.1% formic acid) in 100 min using the micropump at a flow rate of approximately 400 nL/min. Separation was performed on a C18 microcapillary column (BEH C18, 1.7 μm, 75 μm × 100 mm) using the nano separation system. As peptides were eluted from the micro-capillary column, they were electrosprayed into the ESI-MS/MS with the application of a distal 2.1 kV spraying voltage with heated capillary temperature of 200°C. Each scan cycle contained one full-scan mass spectrum (m/z range: 400–2000) and was followed by three data dependent tandem mass spectra. The collision energy of MS/MS analysis was set at 35%.

Yang M.H., Chen M., Mo H.H., Tsai W.C., Chang Y.C., Chang C.C., Chen K.C., Wu H.Y., Yuan C.H., Lee C.H., Chen Y.M, & Tyan Y.C. (2020). Utilizing Experimental Mouse Model to Identify Effectors of Hepatocellular Carcinoma Induced by HBx Antigen. Cancers, 12(2), 409.

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Peptide Separation and Identification by RP-nano-UPLC-ESI-MS/MS

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The complex peptide mixtures were separated by RP-nano-UPLC-ESI-MS/MS. The protein tryptic digests were fractionated using a flow rate of 400 nL/min with a nano-UPLC system (nanoACQUITY UPLC, Waters, Milford, MA) coupled to an ion trap mass spectrometer (LTQ Orbitrap Discovery Hybrid FTMS, Thermo, San Jose, CA) equipped with an electrospray ionization source. For RP-nano-UPLC-ESI-MS/MS, a sample (2 μL) of the desired peptide digest was loaded into the reverse phase column (Symmetry C18, 5 μm, 180 μm × 20 mm) by an autosampler. The RP separation was performed using a linear acetonitrile gradient from 99% buffer A (100% D.I. water/0.1% formic acid) to 85% buffer B (100% acetonitrile/0.1% formic acid) in 100 min using the micropump. The separation is performed on a C18 microcapillary column (BEH C18, 1.7 μm, 75 μm × 100 mm) using the nanoseparation system. As peptides eluted from the microcapillary column, they were electrosprayed into the ESI MS/MS with the application of a distal 2.1 kV spraying voltage with heated capillary temperature of 200°C. Each cycle of one full scan mass spectrum (m/z 400–2000) was followed by four data dependent tandem mass spectra with the collision energy set at 35%.

Yang M.H., Yuan S.S., Huang Y.F., Lin P.C., Lu C.Y., Chung T.W, & Tyan Y.C. (2014). A Proteomic View to Characterize the Effect of Chitosan Nanoparticle to Hepatic Cells: Is Chitosan Nanoparticle an Enhancer of PI3K/AKT1/mTOR Pathway?. BioMed Research International, 2014, 789591.

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Nanoflow HPLC-MS/MS Peptide Analysis

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Resulting peptides were analyzed by RP-nano-HPLC-ESI-MS/MS using a nanoACQUITY HPLC system (Waters, Milford, MA, USA) coupled to an LTQ-Orbitrap Discovery Hybrid FTMS (Thermo Fisher Scientific, Bremen, Germany). For RP-nano-HPLC-ESI-MS/MS, a sample (2 μl) of the desired peptide digest was loaded into the reverse phase column (Symmetry C18, Waters Corporation, Milford, MA, USA, 5 μm, 180 μm × 20 mm) by an autosampler. After 3 min desalting, the precolumn was switched online with the analytical C18 column (BEH C18, 1.7 μm, 75 μm × 100 mm) equilibrated in 99% solvent A (100% D.I. water, 0.1% formic acid) and 1% solvent B (100% acetonitrile, 0.1% formic acid). Peptides were eluted using a linear acetonitrile gradient from 99% solvent A to 85% solvent B during 45 min at 400 nl min⁻¹ flow rate. The LTQ-Orbitrap (Thermo Finnigan, San Jose, CA, USA) was operated in the data-dependent acquisition mode with the XCalibur software. Survey scan MS was acquired in the Orbitrap in the 400–2000 m/z range with the resolution set to a value of 30 000 and collision energy set at 35%. The four most intense ions per survey scan were selected for CID fragmentation, and the resulting fragments were analyzed in the linear trap mass analyzer (Thermo Finnigan). Dynamic exclusion was employed within 60 s to prevent repetitive selection of the same peptide.

Ding D.C., Wen Y.T, & Tsai R.K. (2017). Pigment epithelium-derived factor from ARPE19 promotes proliferation and inhibits apoptosis of human umbilical mesenchymal stem cells in serum-free medium. Experimental & Molecular Medicine, 49(12), e411-.

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Tryptic Peptide Fractionation and LC-MS/MS

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The protein tryptic digests were fractionated using a flow rate of 400 nL/min with a nano-UPLC system (nanoACQUITY UPLC, Waters, Milford, MA) coupled to an ion trap mass spectrometer (LTQ Orbitrap Discovery Hybrid FTMS, Thermo, San Jose, CA) equipped with an electrospray ionization source. For reverse phase nano-UPLC-ESI-MS/MS analyses, a sample (2 μL) of the desired peptide digest was loaded into the trapping column (Symmetry C18, 5 μm, 180 μm × 20 mm) by an autosampler. The reverse phase separation was performed using a linear acetonitrile gradient from 99% buffer A (100% D.I. water/0.1% formic acid) to 85% buffer B (100% acetonitrile/0.1% formic acid) in 100 min using the micropump at a flow rate of approximately 400 nL/min. The separation was performed on a C18 microcapillary column (BEH C18, 1.7 μm, 75 μm × 100 mm) using the nano separation system. As peptides were eluted from the micro-capillary column, they were electrosprayed into the ESI-MS/MS with the application of a distal 2.1 kV spraying voltage with heated capillary temperature of 200°C. Each scan cycle contained one full-scan mass spectrum (m/z range: 400–2000) and was followed by three data dependent tandem mass spectra. The collision energy of MS/MS analysis was set at 35%.

Yang M.H., Chen W.J., Fu Y.S., Huang B., Tsai W.C., Arthur Chen Y.M., Lin P.C., Yuan C.H, & Tyan Y.C. (2017). Utilizing glycine N-methyltransferasegene knockout mice as a model for identification of missing proteins in hepatocellular carcinoma. Oncotarget, 9(1), 442-452.

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