High-Field OrbitrapCreating new possibilities

Thermo Scientific Orbitrap EliteHybrid Mass Spectrometer

Ultrahigh resolution • Faster scanning Higher sensitivity • Complementary fragmentation

The Thermo Scientific Orbitrap Elite hybrid mass spectrometer raises the bar for MS and MSn performance and versatility by combining our premier dual-pressure linear ion trap mass spectrometer with a novel high-field Orbitrap™ mass analyzer. The system delivers greater than 240,000 resolution (FWHM), increased sensitivity, high scan speeds and a larger dynamic range.

High-field Orbitrap mass analyzer for

ultrahigh resolution

The high-field Orbitrap mass analyzer geometry and advanced signal

processing technologies enable resolution of >240,000 FWHM,

a 4x increase over previous technology. This ultrahigh resolution

is especially useful when analyzing samples of high complexity

and targeting analytes of low abundances in applications such as

proteomics, metabolomics and lipidomics.

Faster scanning for UHPLC compatibility

The high-field Orbitrap geometry and advanced signal processing also

provide an up to 4x improvement in scan speed, making the Orbitrap

Elite system more compatible with narrow chromatographic peaks

from UHPLC separations.

The highest resolution, most versatile Orbitrap instrument ever

HCD Collision Cell Transfer MultipoleElectrosprayIon Source S-Lens Octopole

Square Quadrupole with Neutral

BlockerQuadrupoleMass Filter

Low-Pressure Cell

New Detection Electronics

High-PressureCell C-Trap

New High-Field OrbitrapMass Analyzer

Reagent Ion Source

e-

Reagent 1Heated Inlet

Reagent 2Heated Inlet

ETD Option

Higher sensitivity for complex samples

Innovations in the pre-amplifier electronics improve sensitivity. Paired

with the ultrahigh resolution, they provide more comprehensive data

and a deeper look into complex samples.

Fragmentation options increase versatility

In addition to traditional collision-induced dissociation (CID), the

Orbitrap Elite mass spectrometer features higher-energy collisional

dissociation (HCD) that provides superior fragmentation and

higher-quality MS/MS spectra for many types of samples. Optional

electron transfer dissociation (ETD) preserves labile post-translational

modifications of proteins. Intelligent data-dependent decision tree

(DDDT) logic can combine multiple fragmentation techniques in a

single analysis to significantly improve proteome coverage.

A quantum leap in Orbitrap MS performance:

3

The Orbitrap Elite mass spectrometer can analyze complex samples at a greater depth than ever before, helping scientists meet the most demanding challenges in proteomics, metabolomics, lipidomics and metabolism.

The highest resolution, most versatile Orbitrap instrument ever

Key features of the Orbitrap Elite system:

• High-field Orbitrap mass analyzer for higher mass resolution and higher scan speed

• Advanced signal processing for higher resolution

• Improved ion optics for efficient ion injection into the Orbitrap

• New Orbitrap image current pre-amplifier for higher sensitivity

• Velos Pro linear ion trap generation II ion optics with neutral blocking technology for increased robustness

993.3 993.4 993.5 993.6 993.7 993.8 993.9 994.0 994.1 994.2 994.3 994.4 994.5 994.6 994.7 994.8m/z

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Rela

tive

Abun

danc

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]

993.9770R=110221

994.0401R=107426

993.9134R=109564

994.0827R=107785

993.8706R=107582

994.1249R=106063

993.8284R=113310

994.1670R=107915

993.7860R=106257

46620 46650Mass, Da

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e [%

]

46642.586

Analysis of intact yeast enolase (46.64 kDa) on the Orbitrap Elite hybrid MS demonstrates the superior resolution that makes it the new standard for proteomics applications.

Deconvoluted spectrum of yeast enolase (monoisotopic mass 46642.214 Da).

Intact protein analysis

47+ charge state of yeast enolase showing resolution of >100,000 FWHM at m/z 1,000

Orbitrap-based mass spectrometers are an essential tool in many proteomics labs. The enhanced power of the Orbitrap Elite instrument enables new standards of performance for multiple proteomics applications.

Top-down analysis

Maximum resolution of > 240,000 FWHM and complementary

fragmentation modes facilitate better top-down protein identification and

characterization.

PTM analysis

Available electron transfer dissociation (ETD) preserves labile side chains while

creating fragmentation throughout the peptide backbone for better analysis of

post-translational modifications (PTMs).

Protein ID

Faster scanning for more data points across a peak, combined with high

resolution and superior spectral quality, yields more protein identifications in

a single analysis.

Quantitative proteomics

Superior resolution and selectivity of the Orbitrap mass analyzer for both full-

scan MS and MSn enhance relative quantitation analyses such as those using

stable isotope labeling or isobaric mass tags.

A new standard of performance for comprehensive proteomics

5

500 1000 1500 2000m/z

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100 843.9602R=158115

z=2

762.4287R=158642

z=21001.0440R=115639

z=2385.7177R=197410

z=2

600.3526R=185866

z=2664.3820R=171040

z=2537.9891R=189201

z=31093.5867R=125517

z=4

787.4543R=154169

z=11341.7392R=106010

z=51620.8704R=100972

z=3

500 1000 1500 2000m/z

Rela

tive

Abun

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e [%

]

Analysis of histone H4 demonstrates the complementary nature of the HCD and ETD fragmentation techniques in the Orbitrap Elite instrument. Analysis using HCD and ETD in a single run significantly improved sequence coverage over each of the techniques used separately.

Resolution ~ 200,000 FWHM at m/z 400

Resolution > 100,000 FWHM at m/z 1,000

Resolution ~ 200,000 FWHM at m/z 400

Resolution > 100,000 FWHM at m/z 1,000

Q G I T K P A I R R L A R R G G V K R I S G L I Y E E T

R G V L K V F L E N V I R D A V T Y T E H A K R K T V

T A M D V V Y A L K R Q G R T L Y G F G G

S G R G K G G K G L G K G G A K R H R K V L R D N I

HCD ETD

ETD

HCD

Top-down analysis

0

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20 ng

803

563

873

694

933

713

80 ng 200 ng

Num

ber

of Id

entifi

ed P

rote

ins

The superior resolution and spectral quality, as well as the higher scan

speed of the Orbitrap Elite instrument, increase proteome coverage in

complex samples even with very low sample amounts. Here, analysis

of the E. coli proteome labeled with Thermo Scientific Pierce Tandem

Mass Tags demonstrates significant improvement over the already

outstanding performance of the previous-generation Thermo Scientific

LTQ Orbitrap Velos hybrid MS.

Orbitrap EliteLTQ Orbitrap Velos

A new standard of performance for comprehensive proteomics

RT: 1.95 - 6.06

2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0

Time (min)

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3.87

0.1 ppm

386.5 387.0 387.5 388.0

m/z

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Inte

nsity

386.25510

R=251601

387.25830

R=252404

388.26111

R=213904

Even when acquiring MS and MS/MS data, the increased scan speed of the Orbitrap Elite system provides excellent coverage over narrow LC peaks. This analysis of buspirone demonstrates acquisition of full-scan data at a quarter of a million resolution at one Hz. In total, nine scans were acquired during the elution of the peak: five full MS scans and four MS/MS scans.

Buspirone5 full MS scans4 MS/MS scans

BuspironeMS SpectrumR > 250,000

A total solution for metabolism and metabolomics research

The Orbitrap Elite system offers a maximum resolution of >240,000 FWHM that allows complete visibility into sample components and distinguishes them from complex matrix components. Improved sensitivity ensures detection of more metabolites in biological samples. High-quality MSn spectral trees provide extensive structure information for metabolite identification and location of modification sites. Improved robustness enables true 24/7 operation.

Uncompromised performance

• Resolve isobaric species and isotope fine structures for isotope tracing experiments

• Fast scan speed and high resolution improve precision and confidence for quantitation experiments

• MSn de novo structural elucidation for identification of novel metabolites on a UHPLC time scale

• Lower maintenance, and higher productivity when analyzing low-level lipids and metabolites in complex biological matrices

7

High-resolution, accurate-mass full-scan MS spectrum of an oxidative metabolite of buspirone

Total solution for Metabolism and Metabolomics

Metabolism

Thermo Scientific MetWorks and Thermo Scientific Mass Frontier software can

utilize the ultrahigh-resolution accurate-mass data from the Orbitrap Elite system

for streamlined xenobiotic metabolite profiling and identification. The MetWorks™

software integrates acquisition, processing and reporting for metabolite identifica-

tion from LC/MSn analyses and offers in-depth data mining tools for expected

and unexpected metabolites. The Mass Frontier™ software provides chemically

intelligent annotation of MSn spectral trees with automated fragment prediction.

Fragment Ion Search (FISh) in Mass Frontier software allows for automated

localization of biotransformations.

Metabolomics

Thermo Scientific SIEVE and Mass Frontier software utilize the ultrahigh-

resolution accurate-mass data from the Orbitrap Elite for comprehensive analysis

of endogenous metabolites. The SIEVE™ software finds components that have

reproducible differences across multiple sample groups. Optimized component

detection dramatically decreases false positive identifications caused by chemical

background and redundant signals. The SIEVE software searches local and

web-based databases for putative identification. Mass Frontier software provides

confirmation of known compounds through interpretation of MSn spectra, as well

as de novo structural elucidation for unknown compounds.

The Orbitrap Elite system provides accurate mass determination even in complex bile matrices. Here, an oxidative metabolite of buspirone eluting in the window of several bile matrix components was still detected with an absolute mass deviation of 0.5 ppm.

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Inte

nsity

[arb

itrar

y un

its]

512.2684

534.2498

494.2578

550.2151464.2835

412.2851

4000

50,000

100,000

150,000 0.50 ppm

402.2502R=246701

A total solution for metabolism and metabolomics research

BR30

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Africa-Other +27 1 70 1840Australia +61 3 9757 4300Austria +43 1 333 50 34 0Belgium +32 53 73 42 41Canada +1 800 530 8447China +86 10 8419 3588Denmark +45 70 23 62 60

Europe-Other +43 1 333 50 34 0Finland/Norway/Sweden +46 8 556 468 00France +33 1 60 92 48 00Germany +49 6103 408 1014India +91 22 6742 9434Italy +39 02 950 591

Japan +81 45 453 9100Latin America +1 561 688 8700Middle East +43 1 333 50 34 0Netherlands +31 76 579 55 55New Zealand +64 9 980 6700Russia/CIS +43 1 333 50 34 0South Africa +27 11 570 1840

Spain +34 914 845 965Switzerland +41 61 716 77 00UK +44 1442 233555USA +1 800 532 4752

www.thermofisher.com/OrbitrapElite

©2016 Thermo Fisher Scientific Inc. All rights reserved. SimGlycan is a registered trademark of Premier Biosoft International Corp. Tandem Mass Tags is a registered trademark of Proteome Sciences plc. Mass Frontier is a trademark of by HighChem Ltd.. ProSightPC is a trademark of the University of Illinois at Urbana-Champaign. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. Specifications, terms and pricing are subject to change. Not all products are available in all countries. Please consult your local sales representative for details.

Thermo Scientific Xcalibur Data SystemStable operating platformXcalibur™ software is the versatile, easy-to-use data system that controls all Thermo Scientific MS systems. The home page of the Xcalibur software offers easy navigation through the process of instrument setup, sequence setup, and data acquisition.

XtractXtract software deconvolutes isotopically resolved data for intact protein analyses and complex MS/MS spectra acquired in top-down analyses.

Thermo Scientific Proteome Discoverer SoftwareMass informatics platform for protein scientistsProteome Discoverer™ software is a workflow-based proteomics data processing software for in-depth data mining of complex LC-MSn data sets. With the ability to exploit data from different dissociation techniques (CID, HCD, ETD, IRMPD and ECD), Proteome Discoverer software provides extra certainty for peptide and protein identifications. Optional inclusion of multiple search algorithms increases analytical flexibility, and results can now be merged into a single report for easier interpretation.

Thermo Scientific ProSightPC SoftwareProSightPC™ software was developed to address the specific requirements of a top-down and middle-down proteomics strategy. The fragmentation spectra of multiply charged, intact proteins are exceedingly complicated. The software processes high-resolution, accurate-mass data from the Orbitrap Elite MS to produce a list of neutral fragment masses and performs comparisons to proteome databases to identify and characterize proteins.

Thermo Scientific ProteinCenter SoftwareRevealing meaningful biological informationProteinCenter™ software is a web-based data interpretation tool that enables scientists to compare and interpret proteomic data sets and extract meaningful biological information quickly and easily. It provides access to a single database consolidated from more than 20 public databases, including all historical data.

Application-specific software turning data into information

Thermo Scientific Pinpoint SoftwareFacilitating quantitative proteomicsPinpoint™ software facilitates the transition from early-stage biomarker discovery to larger-scale, quantitative verification of putative biomark-ers and general quantitative proteomics. Pinpoint software simplifies the creation of targeted quantitative assays. It allows researchers to leverage previously acquired data from discovery experiments. Pinpoint software largely automates the development of preliminary methods. It enables acquisition and analysis of preliminary data, which is in turn used to optimize the method.

SimGlycan™ SoftwarePredicting glycan and glycopeptide structureSimGlycan software analyzes mass spectrometric data to predict the structure of glycans and glycopeptides. It compares experimental MS/MS data against its own database of theoretical fragments and generates a list of probable candidate structures. Each candidate structure is scored to reflect how closely it matches the experimental data. The software also provides additional biological information for probable glycans and identified glycopeptides.

Thermo Scientific MetWorks Drug Metabolism SoftwareSimplify the interpretation of complex metabolism dataMetWorks software simultaneously searches multiple modifications of one or more parent drugs and interprets simple to complex isotope patterns, or unexpected or low-abundance metabolites.

Thermo Scientific Mass Frontier Spectral Interpretation SoftwareConfident path from spectra to structureMass Frontier software allows confident structural elucidation through chemically intelligent spectral annotation, state-of-the-art fragmentation prediction, and unparalleled spectral and fragmentation mechanism knowledge management.

Thermo Scientific SIEVE Differential Expression SoftwareAnalysis of differential expression based on comparison of LC-MS datasets SIEVE software provides label-free, semi-quantitative differential analysis of proteins, peptides, or metabolites from the comparison of multiple LC-MS data sets. It is a statistically rigorous tool for analyzing data from metabolism or biomarker discovery experiments.