spectrometry

LTQ XL™ Hybrid FT Mass

Unrivaled Performance and Flexibility

Part of Thermo Fisher Scientific linear trap linear ion ™ Additionally, the LTQ Orbitrap XL features a new the LTQ Additionally, collision cell to provide additional flexibility to any MS/MS collision cell to provide additional flexibility to any trap and experiment. can be selected in the linear ion new collision fragmented either in the (CID) or in the cell (HCD). For HCD (Higher Energy Collisional Dissociation) ions are passed through the C-trap into the gas-filled collision cell. Normalized Collision Energy in HCD MS/MS experiments provides reproducible data from instrument to instrument. received the Orbitrap Mass Analyzer ™ PITTCON 2006. PITTCON Editor’s Gold Award at R&D 100 Award in 2006 and the The LTQ Orbitrap technology, the LTQ Orbitrap XL hybrid FTMS Orbitrap XL hybrid LTQ the technology, ™ LEXIBILITY F ND A (Fourier Transform Mass Spectrometer) supports a wide supports a wide Mass Spectrometer) (Fourier Transform from routine compound range of applications most challenging analysis identification to the in complex mixtures. of low level components Schematic of the LTQ Orbitrap XL. Schematic of the LTQ API XL LTQ C-Trap HCD Collision Cell The hybrid FT mass spectrometer combines a linear ion trap The hybrid FT mass spectrometer combines a linear Ions generated by API MS and the Orbitrap mass analyzer. XL followed by axial ejection to the are collected in the LTQ collisionally C-shaped storage trap which is used to store and ions cool ions before injection into the orbital trap. The in the orbital trap are captured transferred from the C-Trap by rapidly increasing the electric field and the detection of the image current from coherent ion packets takes place after the voltages have stabilized. Signals from each of the orbital trap outer electrodes are amplified and transformed into a frequency by fast Fourier transformation which is finally converted into a . and the patented Orbitrap and the patented Based on the fast and highly sensitive Thermo Scientific LTQ XL Scientific LTQ sensitive Thermo the fast and highly Based on RESOLVING POWER, DYNAMIC POWER, RESOLVING SENSITIVITY AND HIGH RANGE, OFFERING OUTSTANDING MASS OUTSTANDING OFFERING ACCURACY, PRINCIPLE OF OPERATION

XL – ERFORMANCE

LTQ Orbitrap XL P RBITRAP

NRIVALED and MALDI capabilities for advanced and small research for advanced proteomics and small molecule collision cell for ultimate flexibility in fragmentation experiments collision cell for ultimate flexibility in fragmentation Future upgrades will include ETD ( Transfer Dissociation) Future upgrades will include ETD (Electron Transfer Features the new HCD (Higher Energy Collisional Dissociation) Features the new HCD (Higher Energy Collisional

• •

LTQ O LTQ U THE MOST CONFIDENT IDENTIFICATION

The analysis of complex protein mixtures is one of the most challenging tasks in the area of proteomics. The key requirements of based methods are a wide dynamic range, outstanding mass accuracy, fast cycle times for MS/MS experiments, and high sensitivity. The LTQ Orbitrap XL meets all of these requirements and provides the most confident protein identification.

THE LTQ ORBITRAP XL PROVIDES: • Superior mass accuracy for lower false positive rates • High sensitivity and dynamic range leading to more protein ID Base peak chromatogram of E. coli total enzymatic digest. • Parallel acquisition mode for optimized productivity • Excellent MS/MS sensitivity

Comparison of the protein identification results () between the LTQ Orbitrap XL and latest Q-TOF technology.

Experimental Method • E. coli total digest (500 ng) • Online nano LC-MS and MS/MS • Optimized productivity with parallel detection • Orbitrap mass analyzer full scan with Ion Trap Top 7 Data Dependent™ MS/MS • Dynamic exclusion

BioWorks™ result of the database search showing the confident identification.

Orbitrap mass analyzer full scan MS at RT 89.4 min with zoom-in. . ™ m/z BLAIS Proteomics Center Boston, MA USA Marto, Ph.D. and Yi Zhang, Ph.D., at R = 30,000 using HCD Dynamic exclusion Mouse cell line iTRAQ labeled Online nano LC-MS and MS/MS Orbitrap mass analyzer full scan 3 MS/MS Data Dependent Top digest sample was provided by Jarrod * The isotopically labeled (iTRAQ) protein • Experimental Method • • • • • iTRAQ reporter ions. : Base peak chromatogram of nano LC-MS and MS/MS analysis.* Base peak chromatogram of nano LC-MS and MS/MS ROVIDES P ELL C This method relies on the measurement of specific reporter ions in the low on the measurement of specific reporter This method relies HCD collision cell of the spectra of target . The new region of MS/MS perform such experiments with excellent Orbitrap XL is ideally suited to LTQ ions and the fragment ratio (S/N) for the reporter sensitivity and signal-to-noise sequence. ions of the peptide An important aspect of proteomics is not only the identification of all the identification is not only aspect of proteomics An important of their determination but also the accurate biological samples in complex quantitation to protein analytical approaches Several relative concentrations. such as iTRAQ including techniques have been developed, XL HCD spectrum for FSALESQLQDTQELLQEENR (MYH9_MOUSE, Myosin-9) in mouse cell line digest derivatized with four iTRAQ reagents.* OLLISION FROM PROTEIN ID TO BIOMARKER DISCOVERY BIOMARKER TO ID PROTEIN FROM HCD C LTQ Orbitrap XL RBITRAP

EW

N LTQ O LTQ

ITH HE More confidence in biomarker research Reliable identification and quantitation in one experiment Reliable identification and quantitation in one Excellent sensitivity and fragmentation efficiency Excellent sensitivity and fragmentation efficiency

W • • • T HIGH QUALITY DATA FOR RELIABLE DE NOVO SEQUENCING

While the extensive use of large-scale genomic sequencing has greatly simplified the task of identifying peptides and proteins by mass spectrometry, the use of de novo sequencing is still required in proteomics research.

BASED ON ULTIMATE PERFORMANCE THE LTQ ORBITRAP XL PROVIDES: • Superior mass accuracy and high resolution leading to confident de novo sequencing results • Multiple collision modes (CID and HCD) for comprehensive structural information

Spectrum of precursor ion with excellent mass accuracy. Zoom-in on low mass range showing detected immonium ions.

Experimental Method • Enzymatic enolase digest • Online nano LC-MS and MS/MS • Orbitrap mass analyzer full scan at R = 60,000 • Data Dependent Top 3 MS/MS using HCD • Dynamic exclusion

Zoom-In on low mass range showing detected immonium ions.

PEAKS™ view MS/MS of 1086.5445 (YGASAGNVGDEGGVAPNIQTAEEALDLIVDAIK). using CID and HCD n incubation in vitro Clozapine Online LC-MS and MS Orbitrap mass analyzer full scan Isotopic pattern triggered MS/MS Dynamic exclusion Experimental Method • • • • • lead to very complex mixtures containing complex mixtures lead to very 270 according to Mass Frontier. m/z in vitro and using MetWorks. for ™ of expected metabolites based on accurate mass Automated identification in vivo : Proposed fragmentation pathway of and Mass Frontier capability n ™ ROVIDES the biological matrix background, the parent drug and all of the metabolites over drug and all of the the parent matrix background, the biological speed of and sensitivity, range. Based on the selectivity, a wide concentration has become the analysis, liquid for metabolite profiling and identification. method of choice The characterization of metabolites plays an important role in drug development. important role in plays an of metabolites The characterization Studies performed ERFORMANCE spectral tree fingerprints to distinguish P n XL P Structural elucidation based on the unique MS Orbitrap XL. of the LTQ CONFIDENT METABOLITECONFIDENT IDENTIFICATION AND PROFILING LTIMATE

U

LTQ Orbitrap XL RBITRAP N O

LTQ O LTQ

ASED even isobaric compounds structural elucidation Improved confidence by MS Reliable metabolite profiling and identification based on accurate mass Reliable metabolite profiling and identification Automated workflows using MetWorks Automated workflows HE

• • • T B CONFIDENT CHARACTERIZATION OF METABOLOMIC PROFILES

The goals of studies are to compare the abundance of the small molecule metabolites in highly complex matrices such as body fluids and tissues. The greatest challenges are the detection of low abundance metabolites amidst a vast background of unchanged metabolites and to confidently identify their structure.

THE LTQ ORBITRAP XL WITH NEW HCD COLLISION CELL PROVIDES: • Outstanding mass accuracy, sensitivity, and dynamic range for metabolic profiling • Confident determination of the identity and structure of metabolites • Determination of differentially expressed metabolites using SIEVE™ in conjunction with Mass Frontier

2-Dimensional scatter plot showing over- and under-expression generated by Spotfire.

Experimental Design • In vivo drug treatment of rats • Controls: untreated day one rat urine • Samples: drug treated day one rat urine • Orbitrap mass analyzer full scan • SIEVE and Spotfire® used to display metabolites that demonstrate statistically significant differences

Zoom into SIEVE frame

Detailed information of over-expressed metabolites. In addition to these offices, Thermo THERMO SCIENTIFIC APPLICATION-SPECIFIC Fisher Scientific maintains a network SOFTWARE–TURNING DATA INTO INFORMATION of representative organizations throughout the world.

Xcalibur™ data system Xtract MetWorks drug Xtract deconvolutes isotopically software Australia Stable operating platform +61 2 8844 9500 • [email protected] resolved data, simplifying complex Simplify the interpretation of complex Xcalibur is the versatile, easy-to-use Austria data system that controls all Thermo MS/MS spectra acquired in top-down, metabolism data +43 1 333 50340 • [email protected] Scientific MS systems. Xcalibur’s intact protein analysis. Specify the MetWorks simultaneously searches Belgium Home Page offers easy navigation mass range, mass resolution, and multiple modifications of one or more +32 2 482 30 30 • [email protected] S/N criteria for deconvolution and parent drugs and interprets simple to Canada through the process of instrument +1 800 532 4752 • [email protected] display in one of four modes: complex isotope patterns, or unex- setup, sequence setup, and data China acquisition. The XReport reporting monoisotopic masses, isotopic pected or low abundance metabolites. +86 10 5850 3588 • [email protected] package simplifies custom reporting pattern, or approved or disapproved Denmark with drag-and-drop functionality. signals. The results can be exported Mass Frontier spectral +45 70 23 62 60 • [email protected] as RAW or ASCII file formats. elucidation software France +33 1 60 92 48 00 • [email protected] ProteinCalculator Turning mass spectral data into results BioWorks protein Germany ProteinCalculator performs in silico Mass Frontier contains a state-of- +49 6103 408 1014 • [email protected] identification software digestion. Specify peptide sequences the-art database and predictive India or import them from a fasta database, Confident protein ID featuring fragmentation module which allows +91 22 6742 9434 • [email protected] the SEQUEST® algorithm you to easily interrogate and assign Italy select post-translational modifications +39 02 950 591 • [email protected] from a list or edit novel PTMs, then BioWorks utilizes the SEQUEST the structure of your compounds. search algorithm to automatically Japan digest them with an enzyme of your +81 45 453 9100 • [email protected] identify proteins by comparing SIEVE differential choosing. The proteolytic fragment expression software Latin America spectra can be saved as RAW data experimental tandem mass +1 608 276 5659 • [email protected] Analysis of differential expression files for comparison with acquired spectrometry (MS/MS) data with Netherlands based on comparison of LC-MSn +31 76 587 98 88 • [email protected] spectra. spectra created from standard protein and DNA databases. datasets South Africa +27 11 570 1840 • [email protected] SIEVE software provides label-free, Spain semi-quantitative differential +34 91 657 4930 • [email protected] expression analysis of proteins, Sweden / Norway / Finland peptides, or metabolites from the +46 8 556 468 00 • [email protected] comparison of multiple LC-MS data Switzerland +41 61 48784 00 • [email protected] sets. It is a statistically rigorous tool UK for analyzing data from metabolism +44 1442 233555 • [email protected] or biomarker discovery experiments. USA +1 800 532 4752 • [email protected] www.thermo.com Installation Requirements

Power Environment Weight 230 Vac ±10% 3 phase, 16 Amps, System averages 2800 W ~600 kg 50/60 Hz, with earth ground for (10,000 Btu/hr) output when the instrument considering air conditioning needs Dimensions 141.4 × 87 × 146.3 cm 120 or 230 Vac single phase with Operating environment must be (H × W × D) earth ground for the data system 15-26 °C (59-78 °F) and relative humidity must be 40-70% with 120 or 230 Vac single phase, 15 Amps, no condensation ©2016 Thermo Fisher Scientific Inc. All rights reserved. iTRAQ is a trademark of Applera Corporation. Mass with earth ground for the water chiller Frontier is a trademark of HighChem, Ltd. PEAKS is a Optimum operating temperature trademark of Bioinformatics Solutions, Inc. Spotfire is a registered trademark of Spotfire, Inc. SEQUEST is a is 18-21 °C (65-70 °F) registered trademark of the University of Washington. Gas All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. One high purity (99.5% pure, flow Specifications, terms and pricing are subject to change. rate 15 L/min) nitrogen gas supply Not all products are available in all countries. Please for the API source consult your local sales representative for details. BR30135_E 09/16M One ultra high-purity helium gas supply (99.998%) with less than 1 ppm each of water, oxygen, and total hydrocarbons for the linear ion trap