Exceptional Analytical Value

LCQ FleetIon Trap LC/MSn

m a s s s p e c t r o m e t r y

Part of Thermo Fisher Scientific

In today’s fast-paced analytical laboratory, your instrument must be easy to use and delivermaximum information with minimum time and sample consumption. With these requirementsin mind, Thermo Fisher Scientific, the pioneer in ion trap technology, introduces the LCQ Fleet™

ion trap mass spectrometer, the latest addition to its award-winning family of ion trap instruments. LCQ Fleet leverages the proven reputation of the LCQ™ ion trap family for excellent MSn

sensitivity, ruggedness and reliability. As the newest member of the LCQ series, this cost effective ion trap mass spectrometer delivers high quality structural information for routineanalysis of the most complex samples, on a high-throughput basis.

Continuing to set standards for ion trap excellence that address your analytical challenges,the LCQ Fleet is designed to meet your needs, whether they are general analytical chemistry,toxicology screening, drug discovery or proteomics. This reliable and easy to use ion trap massspectrometer offers exceptional analytical value while providing confident sample analysis.

LCQ Fleet Ion Trap LC/M

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Unbeatable Rapid and Reliable Detection for Every LabMatch your LC separation with the productivity of the LCQ Fleet

With the Accela™ High Speed LC System, the LCQ Fleet is the perfect tool for highthroughout applications.

Stable and easy-to-use Xcalibur™ software

provides automated LC-MS/MS system

control and data acquisition for complex

sample analysis.

• Data Dependent™ Acquisition – triggers acquisition of MSn spectra onlywhen a compound of interest is detected

• Dynamic Exclusion™ – allows acquisition of MSn spectra fromlower intensity ion species

• Automatic Gain Control™ (AGC) –ensures that the ion trap is always filledwith the optimum number of ions for anyscan type

• WideBand Activation™ – fragments the water loss ion within anMS/MS spectrum, generating more structurally informative spectra

• Normalized Collision Energy™ – compensates for the mass-dependentenergy deposition in ion trap MS/MSexperiments, providing reproducible data from instrument to instrument

• Pulsed-Q Dissociation (PQD)™ –enables trapping of low mass fragment ions

Intelligent AnalysisAutomated features enable all users, from novice

to expert, to easily analyze and interpret sample

analysis data. Application-specific software aids

data processing and compound identification.

• Mass Frontier™ – spectral interpretation and classification software to identify unknowns

• MetWorks™ – automated metabolite identification using spectral trees

• BioWorks™ – protein identification and quantitationfeaturing SEQUEST™

• ToxID – data processing for general unknownscreening

• SIEVE™ – automated label-free differential expression of proteomics and metabolomics data

Technology You Can TrustFrom the inventors of benchtop LC/MS iontrap technology, the LCQ Fleet is the latestaddition to the industry-leading portfolio ofThermo Scientific ion trap mass spectrometersfeaturing more than twenty-five years inbreakthrough technological developments.

In clinical and forensic toxicology, LC-MS is increasingly used for the detection andidentification of unknown xenobiotics ingeneral unknown screening (GUS) studies or systematic toxicological analysis (STA).The inherent capability of the ion trap massspectrometer to provide structural informa-tion using MSn data makes it the preferredinstrument for confident identification ofunknown compounds.

LCQ Fleet is the ideal instrument for thecomprehensive and accurate GUS analysis ina high-throughput environment. The benefitsof the LCQ Fleet for this application include:• High sensitivity and specificity for more

accurate results at a lower detectionlevel compared to traditional methods

• Fast positive/negative switching allowsthe analysis of more compounds with less sample in less time

• Standard normalized collisional energygenerates reproducible spectra for library searching

• Proven reliability and ease of use for LC-MSn

LCQ Fleet Ion Trap LC/M

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Confident General Unknown Screening Intelligent Data Dependent™ acquisition features of the LCQ Fleet enable rapid compound screening for maximum structural information. The fast cycle time andhigh sensitivity of the LCQ Fleet provide the information necessary to confirm theidentity of unknowns in a single analytical run. An automatic library search andretention time confirmation is performed on each fragmentation spectrum, and a one-page summary report is generated for each compound identified. This capabilityis illustrated for the identification of a group of drugs in plasma, using a generalacquisition method consisting of nine scan events with fast positive/negative polarityswitch. The LCQ Fleet allows the identification of groups of GUS compounds using library searches in minutes.

The Solution For Compound Screening and IdentificationMaximize LC/MS information with rapid and reliable compound detection and structural identification

Traditional approaches for the analysis ofnatural products have proven to be time andlabor consuming. The LCQ Fleet significantlyreduces the need for a lengthy pre-purificationprocess while delivering high quality results.It is especially suited for the routine identifi-cation of complex natural products. Thebenefits include: • Reduction or elimination of time-consuming

pre-purification steps with the ability toquickly analyze complex samples

• The fast cycle time of the LCQ Fleetmatches the fast LC separation of theAccela High Speed LC, enabling rapidanalysis of numerous samples

• Excellent MSn spectra quality ensures theconfident structural characterization andcompound identification

• The Ion Max™ source delivers outstandingrobustness for the most demanding analytical applications

• Multiple ionization methods, including ESI,APCI, APPI and more, provide maximumflexibility to achieve comprehensive sample information

• Data can be directly analyzed by MassFrontier™ software for compound identifi-cation and data reporting

In this example, an extract of cinnamonwas studied using a fast chromatographyLC-MSn analysis. Multiple MSn spectra (up to MS5) were acquired in both positiveand negative ionization modes to providecomprehensive structural information of the

component of interest. The fragmentationspectra were analyzed using Mass Frontiersoftware, and the corresponding substruc-tures to all the major peaks were assignedautomatically as illustrated.

Identification of Natural ProductsRobust and fast analysis provides confident structural information

The advancement of proteomics analysisrequires high accuracy and more productivityfrom your experiments. The LCQ Fleet routinelydelivers excellent results for complex proteomics study. It has several features thatmake it well-suited for these applications: • Fast scanning resolves co-eluting

peptides often present in complex protein digests during real time, on-lineLC/MS proteomics analysis

• High sensitivity enables the detection oftrace compounds in a complex mixture

• High quality MSn spectra provide routinepeptide identification with high correlationscores for confident sequence identification

• Pulsed Q Dissociation (PQD) for the detection of low mass fragments foriTRAQ™ analysis

• Fast enhanced scan and zoom scan allowreliable charge states recognition of peptide ions

• High resolution isolation (HRI) allowsaccurate MSn analysis without interferencefrom isotopic ions

A mixture of protein digests was analyzed using the LCQ Fleet ion trap massspectrometer. All the proteins were identifiedvia library search using BioWorks™ withhigh coverage.

LCQ Fleet Ion Trap LC/M

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Complex Proteomics AnalysisConfident peptide identification

Protein % Coverage

Apomyoglobin 36

Lysozyme 48

α-Lactalbumin 33

Cytochrome C 50

Ovalbumin 15

Bovine serum albumin 34

Carbonic anhydrase 18

Product Specifications

Hardware Features

Ion Max-S API Source• Enhanced sensitivity and ruggedness• Sweep Gas™ reduces chemical noise• 60° interchangeable ion probe orientation• Removable metal ion capillary tube provides

vent-free maintenance

Options• ESI source compatible with liquid flow rates

of <1 µL/min to 1 mL/min, without splitting• APCI source compatible with liquid flow

rates of 50 µL/min to 2 mL/min, withoutsplitting

• APCI/APPI source compatible with liquidflow rates of 50 µL/min to 2 mL/min, without splitting

• Metal needle option for high- and low-flowanalyses

• HESI source compatible with liquid flowrates of <1 µL/min to 1 mL/min, withoutsplitting

• Nanospray II source supports static packedtip and dynamic nanospray experiments,compatible with liquid flow rates of 50 nL/min*to 2 µL/min

* Lower limit is dependent on gauge of needle used

Transfer Ion Optics• Advanced multipole ion guides• High stability and ion transmission efficiency

Vacuum System• Differentially-pumped vacuum system to

10-5 Torr• Split-flow turbomolecular pump controls

vacuum in three regions• High-vacuum machined aluminum analyzer

chamber

Detection System• Patented conversion dynode detector• Off-axis continuous dynode electron

multipliers with extended dynamic range• Digital electronic noise discrimination• High-efficiency radial ion ejection

Integrated Divert Valve• Fully-automated data system control

enables user to divert to waste the solventfront, gradient end point and any other portionof the HPLC run

• User-definable default state of the valve,either “to waste” or “to source”

Integrated Syringe Pump• Syringe Pump allows automated infusion

under data system control

Software Features

Data System• Xcalibur processing and instrument

control software• LCQUAN™ quantification package• Microsoft® Office XP software package• Microsoft Windows® XP operating system• High-performance PC with Intel® Pentium®

microprocessor• High-resolution LCD color monitor

Scan Functions• Full-scan feature provides full-scan mass

spectra for sensitive analyses and producesspectra for rapid screening of unknown compounds

• Selected Ion Monitoring (SIM) monitorsselected ions for target compound analysis

• Full-scan MS/MS produces full-scan production spectra at sensitivities higher than anyion trap mass spectrometer

• Selected Reaction Monitoring (SRM) for a traditional LC/MS/MS quantitative analytical experiment

• MSn for multi-stage MS experiments to probethe structure of ions

• ZoomScan™ a high-resolution, full-rangescan to resolve isotopic envelopes which isoften used for charge state determination ofpeptides and ionization state determinationof organometallics

• TurboScan™ an ultra-fast scan to improvesignal-to-noise and sampling rate

Exclusive Technologies• Unique, patented Automatic Gain Control

(AGC) ensures that the ion trap is alwaysfilled with the optimum number of ions forany scan type

• Dynamic Exclusion™ allows acquisition ofMS/MS and MSn spectra from lower intensityion species

• WideBand Activation™ generates morestructurally informative spectra

• Normalized Collision Energy™ compensatesfor the mass-dependent energy depositioncharacteristics of ion trap mass spectrometersin MS/MS experiments, providing reproducibledata from instrument to instrument

• Pulsed-Q Dissociation (PQD)™ – enablestrapping of low mass fragment ions

System Specifications

MS/MS Sensitivity

Electrospray Ionization (ESI) – A loop injection of 2 µL of a 1 pg/µL solutionof reserpine (2 picograms, 3.28 picomolestotal sample) at a flow of 400 µL/min of 50%isopropyl alcohol/50% water will produce aminimum signal-to-noise ratio of 100:1, forthe transition of the isolated protonatedmolecular ion at m/z 609 to the largest twoproduct ions, 397 and 448, when the massspectrometer is operated at unit resolutionin the full-scan MS/MS mode, scanning theproduct ion spectrum from m/z 165 – 615.

Atmospheric Pressure Chemical

Ionization (APCI) – A loop injection of 2 µLof a 1 pg/µL solution of reserpine (2 picograms,3.28 picomoles total sample) at a flow of400 µL/min of 50% isopropyl alcohol/50%water will produce a minimum signal-to-noiseratio of 100:1, for the transition of the isolated protonated molecular ion at m/z 609to the largest two product ions, 397 and 448,when the mass spectrometer is operated atunit resolution in the full-scan MS/MS mode,scanning the product ion spectrum from m/z 165 – 615.

Installation RequirementsPower• One 230 Vac ±10.0%, 15 Amps, 50/60 Hz,

single phase, with earth ground dedicatedto the instrument

• 120 or 230 Vac single phase, with earthground for the data system

Gas• One high-purity (99% pure, flow rate 15 L/min)

nitrogen gas supply for the API source• One ultra high-purity helium gas supply

(99.998% pure) with less than 1 ppm eachof water, oxygen, and total hydrocarbons forthe mass analyzer

Environment• System averages 2300 W (8000 Btu/h) out-

put when considering air conditioning needs• Operating environment must be 15-27 °C

(59-80 °F) and relative humidity must be 40-80% with no condensation

• Optimum operating temperature is 18-21 °C(65-70 °F)

Dimensions / Weight• MS: 56 cm x 79 cm x 59 cm (h x w x d)• MS: ~120 kg• Roughing pumps: 38.6 kg

Performance Specifications

Mass Range• m/z 15 – 200• m/z 50 – 2000• m/z 100 – 4000

Resolution• Down to 0.3 FWHM (full width half

maximum) with Zoom Scan

Scan Power• MSn, for n = 1 through 10• Contact Closure• Start In/Out• Start Out is programmable

Analog Inputs• One (1) analog Input (0-1 V)• One (1) analog Input (0-10 V)

BR62395_05/07M

Thermo Finnigan LLC, San Jose, CA USA is ISO Certified.

©2007 Thermo Fisher Scientific Inc. All rights reserved.SEQUEST is a registered trademark of the University ofWashington; Mass Frontier is a trademark of HighChem,Ltd.; Intel and Pentium are registered trademarks ofIntel Corporation; Microsoft and Windows are regis-tered trademarks of Microsoft Corporation; iTRAQ is atrademark of Applera Corporation. All other trademarksare 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. Pleaseconsult your local sales representative for details.

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