Product Specifications

experiments such as HCD n editor also contains a comprehensive library of application-specific templates for commonly performedanalyses. complex MS followed ETD by for glycopeptide characterization or HCD followed CID by for small-molecule structural analysis. The ultrahigh resolution of the Orbitrap mass analyzer increases certainty of analytical results, enabling molecular-weight determination for intact proteins and confident resolution of isobaric species. The unsurpassed scan rate and resolution of the system are especially useful when dealing with complex and low-abundance samples proteomics, in metabolomics, glycomics, lipidomics, and applications. similar The intuitive user interface of the tune editor and method editor makes instrument calibration and method development The method easier.

acquisition n , with fragment n , with subsequent mass n Tribrid architectureTribrid combines quadrupole, Multiple fragmentation techniques—CID, Parallelization of MS and MS Next-generation ion sources and ion Innovative instrument control software linear ion trap, and Orbitrap mass analyzers HCD, and optional ETD—are available at any stage of MS analysis either in the ion trap or Orbitrap massanalyzer to maximize the amount of high-quality dataacquired optics increase system ease of operation robustness and makes methods setup easier, more powerful, and operation more intuitive complex PTMs complex qual/quan comprehensive to workflows. availabilityThe multipleof fragmentation techniques—CID, HCD, and ETD—at any stage of MS ion detection either in the ion trap or Orbitrap mass offers analyzer, a new level of versatility and performance for the most challenging applications. Users can perform •  •  •  •  •  The Orbitrap MS Fusion can Tribrid perform a wide variety of analyses, from in-depth discovery experiments to characterization of

Unmatched analytical performance, Unmatched revolutionary MS architecture architecture ™ mass ™ Tribrid ™ OrbitrapFusion

Thermo Scientific OrbitrapFusion Spectrometer Mass Tribrid ™ MASS SPECTROMETRY molecular composition more thoroughly. more composition molecular quantify them more accurately, and elucidate high complexity,or difficult-to-analyze chemical structure—to identify more compounds faster, challenging samples—samples abundance, challenging low of that unprecedented delivers depth analysis. of It enables life scientists working with even the most revolutionary Thermo Scientific spectrometer the best combines quadrupole, of Orbitrap, and linear ion trap mass analysis in a The Thermo Scientific 2

The optional Thermo Scientific™ EASY-ETD™ Dual-Pressure Linear Ion Trap Performance Characteristics ion source uses Townsend discharge • High-pressure cell for precursor ion Linear Ion Trap Mass Range ionization to generate a highly stable reagent isolation from 0.2 amu to full mass range Standard – m/z 50–2,000 ion flux. The source is very compact, fitting • Collision-induced dissociation (CID) and High Mass – m/z 200–4,000 inside the mass spectrometer. Intelligent, electron-transfer dissociation (ETD) automated precursor ion sorting routines, Orbitrap Mass Range reagent filtering using the quadrupole mass • Low-pressure cell for improved scan speed, Up to m/z 6000 without precursor ion resolving power, and mass accuracy filter, and charge-state-specific calibration of selection • Dual-dynode detector with high linear ETD reaction time maximize the quality of dynamic range for improved quantitation Resolution ETD spectra. and a large surface area for increased 15,000–450,000 (FWHM) at m/z 200 lifespan and robustness Hardware Specifications Scan Rate (under defined conditions) Vacuum System n Ion Source Orbitrap MS up to 15 Hz • Split-flow turbomolecular pump controlling Ion trap MSn up to 20 Hz Thermo Scientific™ EASY-Max NG™ vacuum in multiple regions Mass Accuracy (under defined conditions) Ion Source • Precise and accurate low mTorr pressure • Outstanding performance without control in the ion-routing multipole <3 ppm RMS using external calibration adjustments • Differentially pumped to ~3 × 10-4 Torr in <1 ppm RMS using internal calibration • Automatic gas and electrical connections the ion trap chamber MS/MS Electrospray Ionization (ESI) on installation -10 • Differentially pumped to <2 × 10 Torr in Ion Trap Sensitivity • Enhanced exhaust port efficiently removes Orbitrap mass analyzer 2 μL of a 50 fg/μL solution of reserpine solvent vapor, improving uptime and (100 fg total) injected at a flow of 500 μL/min reducing chemical noise Options will produce a minimum signal-to-noise ratio ™ ™ Ion Optics Thermo Scientific Ion Max NG Ion Source of 100:1 for the transition of the isolated • Adjustable heated electrospray ionization protonated molecular ions at m/z 609 to S-Lens (HESI) probe for ultimate sensitivity the largest two product ions, m/z 397 and • Progressively spaced stacked-ring ion • Flow rates from 1 μL/min up to m/z 448, when the mass spectrometer is guide (S-Lens) captures and efficiently <2,000 μL/min operated at unit resolution in the full-scan focuses ions in a tight beam MS/MS mode, m/z 165–615. The test • APCI/APPI probe compatible with liquid requires the HESI probe. • Large variable spacing between electrodes flow rates of 50 μL/min to 2 mL/min provides better pumping efficiency and without splitting Dynamic Range improved ruggedness Thermo Scientific™ NanoSpray Flex NG™ >5,000 within a single scan, guaranteeing • Automatic tuning program optimizes specified mass accuracy transmission Ion Source • Supports static packed-tip and dynamic MS Scan Power Active Beam Guide nanoelectrospray experiments MSn, for n = 1 through 10 • Reduces noise by preventing neutrals and • Compatible with liquid flow rates of Synchronous Precursor Selection high-velocity clusters from entering the 50 nL/min to 2 μL/min quadrupole mass filter Up to 15 precursors per MS2 scan, for MS3 ™ ™ • Axial field along the length of the rods Thermo Scientific EASY-Spray Ion Source analysis only improves ion transfer robustness • Maximum nanoelectrospray performance Multiplexing Using Ion-Routing Multipole with no need for adjustments Quadrupole Mass Filter Up to 10 precursors per scan using ™ ™ • Precursor ion selection with high ion Thermo Scientific EASY-ETD Ion Source quadrupole mass filter transmission • Generates fluoranthene anions for electron Polarity Switching • Precursor ion isolation window widths from transfer dissociation (ETD) One full cycle in 1.1 sec (one full scan in 0.4 amu to 20 amu • Townsend discharge ionization is extremely positive mode and one full scan in negative stable and robust Ion-Routing Multipole mode at resolution setting of 35,000) • Compact size, located entirely within the • Higher-energy collisional dissociation footprint of the instrument ETD Option (HCD) cell • Active reagent ion filtering using 3 μL/min infusion of a 1 pmol/μL solution of • Ion storage with or without fragmentation mass-resolving quadrupole angiotensin I will produce an electron-transfer • Efficient and stable ion transfer between dissociation fragmentation efficiency of >15% ™ ™ the ion-routing multipole and the Orbitrap Thermo Scientific EASY-IC Ion Source Analog Inputs and linear ion trap mass analyzers • Generates internal calibrant ions for real-time mass calibration on every One (1) analog input (0–1 V), Orbitrap Mass Analyzer spectrum One (1) analog (0–10 V) • Nitrogen-filled C-Trap • Provides <1 ppm RMS mass accuracy • Ultra-high-field Orbitrap mass analyzer with resolving power up to 450,000 FWHM and isotopic fidelity up to 240,000 FWHM at m/z 200 • Scan rate up to 15 Hz • 16-bit signal digitization 3

Figure 1. Orbitrap Fusion ion path

Software Features Data System Exclusive Technologies • High-performance PC with Intel® • Dynamic scan management allows for • Data-dependent neutral-loss experiment microprocessor intelligent, real-time scheduling, triggers MS3 scans on only MS/MS • High-resolution LCD color monitor parallelization, and prioritization of the scan product ions with a predefined neutral loss events. It also enables selection, sorting, • Microsoft® Windows® 7 operating system • Isolation window offset allows for custom and routing of precursors to different centering of the isolation window when • Microsoft Office 2010 software fragmentation modes and analyzers based working with broad isotopic distributions • Thermo Scientific™ Xcalibur™ processing on user-selected parameters, including precursor m/z, intensity, and/or charge. • Quanfirmation experiment uses synchronous and instrument control software HR/AM SIM for quantitation with full-scan • Tune editor for system calibration, • Precursor fragmentation can take place in MS/MS in the ion trap for precursor diagnostics, and manual data acquisition the ion-routing multipole (HCD) or in the identity confirmation ion trap (CID, ETD) with fragment detection • Method editor with comprehensive in the linear ion trap or Orbitrap mass Optional Application-Specific Software application-specific template library and analyzers at any stage of MSn analysis ™ ™ drag-and-drop user interface to facilitate • Thermo Scientific Compound Discoverer method development • Dynamic exclusion allows acquisition of software – integrated solution for MS/MS and MSn spectra from lower-intensity small-molecule structural identification Operation Modes ion species • Thermo Scientific™ Mass Frontier™ • Top-speed mode maximizes the number of • Automatic gain control (AGC) ensures that software – predictive fragmentation high-quality MSn spectra from each cycle the ion trap is always filled with the software for spectral interpretation and by intelligently scheduling MS and optimum number of ions for any scan type classification software to identify data-dependant MSn scans based on a • Normalized collision energy for both CID unknowns user-definable time between adjacent and HCD fragmentation techniques • Thermo Scientific™ Pinpoint™ software – survey scans ensures reproducible data from instrument comprehensive targeted protein • Synchronous MS3 precursor selection to instrument quantitation platform significantly increases the number of ™ ™ Advanced Data-Dependent Experiments • Thermo Scientific ProSightPC software – peptides accurately quantified in isobaric stand-alone software for analyzing mass tagging experiments • Dynamic scan management facilitates a wide top-down intact-protein data, but also • Quanfirmation experiment uses synchronous range of data-dependent experiments with middle-down and bottom-up data high-resolution, accurate-mass (HR/AM) real-time selection, prioritization, and routing ™ of precursors to different fragmentation • Thermo Scientific Protein Deconvolution selected-ion monitoring (SIM) for quantitation software – intact-protein analysis platform and sensitive full-scan MS/MS in the ion modes and analyzers based on user-selected ™ ™ trap for precursor identity confirmation parameters including precursor m/z, intensity, • Thermo Scientific Proteome Discoverer and/or charge software – flexible, expandable platform for • Parallelization maximizes the amount of • Fragment ion or neutral-loss-triggered MSn the analysis of qualitative and quantitative high-quality data acquired by synchronizing proteomics data operation of the quadrupole mass filter, experiments including at the same MSn level ™ ™ ion-routing multipole, and ion trap and • Synchronous MS3 precursor selection • Thermo Scientific SIEVE software – Orbitrap mass analyzers significantly increases the number of label-free, semi-quantitative differential peptides accurately quantified in isobaric analysis of highly complex data sets mass tagging experiments Product Specifications Product Installation Requirements Power • Instrument – 230 Vac ± 10% single phase, 15 Ampere, 50/60 Hz, with earth ground • Data system – 120 or 230 Vac single phase, 50/60 Hz, with earth ground Gas • Ultra-high-purity helium (99.999%) with less than 1 ppm each of water, oxygen, and total hydrocarbons • High-purity nitrogen (99.5% pure, flow rate 15 L/min) nitrogen gas supply for the ion source and C-Trap • For ETD/IC options: ultra-high-purity nitrogen (UHP, 99.999%) with less than one ppm each of water and oxygen Size 1270 × 767 × 703 mm (w, d, h). The system comes mounted on a 1320 × 788 × 726 mm (w, d, h) table, similar to a standard lab bench Weight 318 kg (700 pounds) with table but without data system, vacuum rough pumps, and optional items Environment • System averages 2,800 W (10,000 Btu/hr) output • Operating environment must be 16–26 °C (59–78 °F) and relative humidity must be 50–80% with no condensation • Optimum operating temperature is 18–21 °C (65–70 °F)

Figure 2. Orbitrap Fusion MS dimensions

For Research Use Only. Not for use in diagnostic procedures. www.thermoscientific.com ©2013 Thermo Fisher Scientific Inc. All rights reserved. ISO is a trademark of the International Standards Organization. Intel is a registered Thermo Fisher Scientific, trademark of Intel Corporation. Microsoft and Windows are registered trademarks of Microsoft Corporation. All other trademarks are the San Jose, CA USA is property of Thermo Fisher Scientific Inc. and its subsidiaries. Specifications, terms and pricing are subject to change. Not all products are ISO 9001:2008 Certified. available in all countries. Please consult your local sales representative for details.

Africa-Other +27 11 570 1840 Europe-Other +43 1 333 50 34 0 Japan +81 45 453 9100 Spain +34 914 845 965 Australia +61 3 9757 4300 Finland/Norway/Sweden Latin America +1 561 688 8700 Switzerland +41 61 716 77 00 Austria +43 1 333 50 34 0 +46 8 556 468 00 Middle East +43 1 333 50 34 0 UK +44 1442 233555 Belgium +32 53 73 42 41 France +33 1 60 92 48 00 Netherlands +31 76 579 55 55 USA +1 800 532 4752 Canada +1 800 530 8447 Germany +49 6103 408 1014 New Zealand +64 9 980 6700 China +86 10 8419 3588 India +91 22 6742 9434 Russia/CIS +43 1 333 50 34 0 Denmark +45 70 23 62 60 Italy +39 02 950 591 South Africa +27 11 570 1840 PS63844_E 06/13S