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Orbitrap platform

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The Orbitrap platforms are high-resolution mass spectrometry instruments developed by Thermo Fisher Scientific. They utilize the Orbitrap mass analyzer, which is based on the principle of trapping ions in an electrostatic field and measuring their oscillation frequency to determine their mass-to-charge ratio.

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Lab products found in correlation

Captive spray nano electrospray source, by Bruker (1 mentions) Solarix 15t ft icr ms, by Bruker (1 mentions)

5 protocols using orbitrap platform

1

Metabolic Profiling of C. albicans

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An overnight culture of C. albicans was diluted into YNB-CSM-2% glucose media at an OD600 of 0.25, grown for 3hr to mid-log phase, and then split into parallel 5 mL cultures for treatment with compounds (DMSO, 20µM rotenone, 1µM antimycin, 5mM potassium cyanide, 20µM oligomycin, 25 µg/mL 2,4-dinitrophenol, 32 µM FCCP, 2.5 µM ML316). After growth with compounds for the indicated time intervals, cultures were pelleted, washed once in PBS, and frozen in liquid nitrogen. Polar metabolites were extracted by re-suspending cells in 600 µL methanol, 300 µL water, and 400 µL chloroform, and adding 100 µL of glass beads before vortexing for 60 seconds. Samples were then centrifuged for 10 minutes at 13,000g, and the supernatant (polar) layer was moved to a new microcentrifuge tube, and evaporated by Speedvac. Samples were then subjected to LC-MS/MS profiling on a Thermo Orbitrap platform, as described previously.37 (link)
McLellan C.A., Vincent B.M., Solis N.V., Lancaster A.K., Sullivan L.B., Hartland C.L., Youngsaye W., Filler S.G., Whitesell L, & Lindquist S. (2017). Inhibiting mitochondrial phosphate transport as an unexploited antifungal strategy. Nature chemical biology, 14(2), 135-141.
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2

Metabolic Profiling of C. albicans

Cited 1 time
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An overnight culture of C. albicans was diluted into YNB-CSM-2% glucose media at an OD600 of 0.25, grown for 3hr to mid-log phase, and then split into parallel 5 mL cultures for treatment with compounds (DMSO, 20µM rotenone, 1µM antimycin, 5mM potassium cyanide, 20µM oligomycin, 25 µg/mL 2,4-dinitrophenol, 32 µM FCCP, 2.5 µM ML316). After growth with compounds for the indicated time intervals, cultures were pelleted, washed once in PBS, and frozen in liquid nitrogen. Polar metabolites were extracted by re-suspending cells in 600 µL methanol, 300 µL water, and 400 µL chloroform, and adding 100 µL of glass beads before vortexing for 60 seconds. Samples were then centrifuged for 10 minutes at 13,000g, and the supernatant (polar) layer was moved to a new microcentrifuge tube, and evaporated by Speedvac. Samples were then subjected to LC-MS/MS profiling on a Thermo Orbitrap platform, as described previously.37 (link)
McLellan C.A., Vincent B.M., Solis N.V., Lancaster A.K., Sullivan L.B., Hartland C.L., Youngsaye W., Filler S.G., Whitesell L, & Lindquist S. (2017). Inhibiting mitochondrial phosphate transport as an unexploited antifungal strategy. Nature chemical biology, 14(2), 135-141.
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3

Orbitrap-based Bottom-up Proteomic Analysis

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All bottom-up proteomic LC-MS/MS data were collected using Orbitrap platforms (Thermo Scientific, San Jose, CA, USA) and were completed using standard approaches detailed in the Supporting Information.
Ryan D.J., Patterson N.H., Putnam N.E., Wilde A.D., Weiss A., Perry W.J., Cassat J.E., Skaar E.P., Caprioli R.M, & Spraggins J.M. (2019). MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. Analytical chemistry, 91(12), 7578-7585.
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4

Ancient Ostrich Eggshell Proteomics

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Ostrich eggshell samples were ground and bleached for 72 hr (NaOCl 12% wt/vol) and rinsed thoroughly before demineralization. Amino acid and mass spectrometry analysis of ancient proteins was conducted using published techniques (Buckley et al., 2009 (link); Crisp et al., 2013 (link)). Modifications include the use of trypsin and elastase as digestion enzymes for separate preparations (Welker et al., 2015 (link)). Liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses were performed on Thermo Scientific Orbitrap platforms. Resulting spectra were searched against the Struthioniformes genomes using PEAKS (version 7.5 [Ma et al., 2003 (link)]). For PEAKS, FDR rate was set at 0.5%, with proteins accepted with −10lgp scores ≥ 40 and ALC (%) ≥ 80. A combination of minimization and conventional MD using the DL_Poly Classic code was used to explore possible protein–calcite binding geometries (Freeman et al., 2011 (link)).
Demarchi B., Hall S., Roncal-Herrero T., Freeman C.L., Woolley J., Crisp M.K., Wilson J., Fotakis A., Fischer R., Kessler B.M., Rakownikow Jersie-Christensen R., Olsen J.V., Haile J., Thomas J., Marean C.W., Parkington J., Presslee S., Lee-Thorp J., Ditchfield P., Hamilton J.F., Ward M.W., Wang C.M., Shaw M.D., Harrison T., Domínguez-Rodrigo M., MacPhee R.D., Kwekason A., Ecker M., Kolska Horwitz L., Chazan M., Kröger R., Thomas-Oates J., Harding J.H., Cappellini E., Penkman K, & Collins M.J. (2016). Protein sequences bound to mineral surfaces persist into deep time. eLife, 5, e17092.
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5

Offline and Online LC-MS/MS Protocol

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All of the offline top-down and bottom-up LC-MS/MS data were collected using Orbitrap platforms (Thermo Scientific, San Jose, CA, USA) and were completed using standard approaches as described in supplemental information. For the online LC-MS experiments, proteins were eluted using an analytical column which was packed with 20 cm of C4 reverse phase material (Halo Protein C4, 3.4 μm, 400Å) with a laser-pulled emitter tip. Proteins were loaded on the capillary reverse phase analytical column (360 μm O.D. × 150 μm I.D.) using a Waters nanoACQUITY UPLC (Waters Corporations, Milford, MA, USA) where mobile phase A consisted of 0.1% formic acid, 99.99% water, and mobile phase B consisted of 0.1% formic acid, 99.99% acetonitrile, eluting at 0.600 μL/min. Ions were generated using a Bruker Captive Spray nanoelectrospray source (Bruker Daltonics, Billerica, MA, USA) and directed into a Bruker SolariX 15T FTICR MS (Bruker Daltonics, Billerica, MA, USA). The mass spectrometer was set to scan from m/z 230-2,000, with a file size of 1M yielding a resolving power of 150,000 at m/z 400 (FID length: 0.5243 s). Ion optics were tuned as follows: accumulation hexapole (2 MHz, 1200 Vpp), time-of-flight delay (0.8 ms), funnel RF amplitude (280 Vpp), transfer optics (4 MHz, 290 Vpp), and ICR cell (sweep excitation power: 18%).
Ryan D.J., Nei D., Prentice B.M., Rose K.L., Caprioli R.M, & Spraggins J.M. (2018). Protein Identification in Imaging Mass Spectrometry through Spatially Targeted Liquid Micro-Extractions. Rapid communications in mass spectrometry : RCM, 32(5), 442-450.
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