System User Guide - Sciex

1 6500 and 6500+ Series of InstrumentsSystem User GuideAugust 2015 RUO-IDV-05-2095-AThis document is provided to customers who have purchased Sciex equipment to use in the operation of such Sciex equipment. This document is copyright protected and any reproduction of this document or any part of this document isstrictly prohibited, except as Sciex may authorize in that may be described in this document is furnished under a license agreement. It is against the law to copy, modify,or distribute the software on any medium, except as specifically allowed in the license agreement. Furthermore, the licenseagreement may prohibit the software from being disassembled, reverse engineered, or decompiled for any purpose. Warrantiesare as stated of this document may make reference to other manufacturers and/or their products, which may contain parts whosenames are registered as trademarks and/or function as trademarks of their respective owners.

2 Any such use is intended onlyto designate those manufacturers' products as supplied by Sciex for incorporation into its equipment and does not implyany right and/or license to use or permit others to use such manufacturers' and/or their product names as warranties are limited to those express warranties provided at the time of sale or license of its products and are Sciex ssole and exclusive representations, warranties, and obligations. Sciex makes no other warranty of any kind whatsoever,expressed or implied, including without limitation, warranties of merchantability or fitness for a particular purpose, whetherarising from a statute or otherwise in law or from a course of dealing or usage of trade, all of which are expressly disclaimed,and assumes no responsibility or contingent liability, including indirect or consequential damages, for any use by the purchaseror for any adverse circumstances arising research use only.

3 Not for use in diagnostic Sciex is doing business as trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective Sciex is being used under license. 2015 AB SCIEXAB Sciex Pte. 33, #04-06 Marsiling Ind Estate Road 3 Woodlands Central Indus. 739256 System User Guide6500 and 6500+ Series of InstrumentsRUO-IDV-05-2095-A2 of 181 Chapter 1 Operational Precautions and Safety and New Mains Earth Safe and Use and 2 Hazard Health and Safety , Indicators, and Labels: , Indicators, and Labels: Mass Symbols and 3 Principles of of Operation Hardware ..28 Analyst Software Overview ..30 Theory of Operation Analyst 4 Operating Instructions Sample 5 Operating Instructions Hardware.

4 44 Start Up the the Mass Down the and 6500+ Series of InstrumentsSystem User Guide3 of 181 RUO-IDV-05-2095-AContentsPlumb the Mass Spectrometer ..47 Adjust the Integrated Syringe Pump the Diverter Valve in Injector the Diverter Valve in Diverter 6 Operating Instructions Hardware Profiles and a Hardware Devices to a Hardware Hardware Profile and Projects and Between Projects and Project Up the API Instrument the API Instrument 7 Operating Instructions Tune and the Mass the Verifying or Adjusting Performance 8 Operating Instructions Automatic Automatic of Sample Optimize for an Analyte Using the Presence of Automatic MS and MS/MS Optimization Using Infusion with aPrecursor Ion and an Unknown Product the Optimization Optimize for an Analyte Using 9 Operating Instructions Acquisition an Acquisition Method Using the Acquisition Method the

5 Syringe an a an Experiment into a an Experiment within a Scan Scan Spectral Data 10 Operating Instructions Batches ..86 Set Queue Sets and Samples to a a Sample or Set of Sample User Guide6500 and 6500+ Series of InstrumentsRUO-IDV-05-2095-A4 of 181 ContentsAcquire Sample Locations in the Batch Vial Positions Using the Locations Tab (Optional)..92 Set Quantitation Details in the Batch Editor (Optional)..93 Stop Sample and Submit Batch a Batch as a Text a Batch as a Text Editor Right-click States and Device Instrument and Device Status Right-click 11 Operating Instructions Analyze and Process Quantitative Results Methods and Results a Method Using the Quantitation Method a Results Table Using the Quantitation a Standard Table Right-click Review and Manual Integration of Integrate Review Right-Click Calibration Calibration Curve Right-Click the Statistics for Standards and Results Between 12 Operating Instructions Analyze and Process Data Between Samples in a Data Experimental Data in ADC Basic Quantitative TICs from a a Spectrum from a Generating an XIC Using a Selected

6 An XIC Using the Maximum an XIC Using Base Peak and 6500+ Series of InstrumentsSystem User Guide5 of 181 RUO-IDV-05-2095-AContentsExtract Ion by Selecting DAD the In on the In on the 13 Reporter User 14 Service and Maintenance Maintenance the the of the Mass the Curtain the Front of the Orifice the Mass Spectrometer Back in the Source Exhaust Drain and Handling ..148 Chapter 15 Mass Spectrometer A Operating Instructions Manual Manual Compound Scan Optimize an the Presence of MS-Specific the Product Ions for Collision Cell Exit Potential for each Product Optimize the Ion Source and Gas the Ion the Ion Source B 6500 and 6500+ Series System C Calibration Ions and D Toolbar User Guide6500 and 6500+ Series of InstrumentsRUO-IDV-05-2095-A6 of 181 ContentsRevision and 6500+ Series of InstrumentsSystem User Guide7 of 181 RUO-IDV-05-2095-AContentsNote: Before operating the System , carefully read all the sections of this section contains general safety-related information and provides regulatory compliance information.

7 It alsodescribes potential hazards and associated warnings for the System and the precautions that should be taken tominimize the addition to this section, refer to Hazard Symbols on page 18 for information about the symbols and conventionsused in the laboratory environment, on the System , and in this documentation. Refer to the Site Planning Guidefor site requirements, including AC mains supply, source exhaust, ventilation, compressed air, nitrogen, androughing pump Safety InformationTo prevent personal injury or System damage, read, understand, and obey all of the safety precautions, warningsin this document, and labels on the mass spectrometer. These labels are shown with internationally recognizedsymbols. Failure to heed these warnings could result in serious safety information is intended to supplement federal, state, provincial, and local environmental health andsafety (EHS) regulations.

8 The information provided covers System -related safety with regard to the operation ofthe mass spectrometer. It does not cover every safety procedure that should be practised. Ultimately, the user andthe organization are responsible for compliance with federal, state, provincial, and local EHS regulations and formaintaining a safe laboratory to the appropriate laboratory reference material and standard operating ComplianceThis System complies with the regulations and standards listed in this section. Refer to the Declaration of Conformityincluded with the System and the individual System components for dated references. Applicable labels have beenaffixed to the and new zealand Electromagnetic Compatibility (EMC): Radio Communications Act 1992 as implemented in thesestandards: Electromagnetic Interference AS/NZS CISPR 11/ EN 55011/ CISPR 11 (Class A) System User Guide6500 and 6500+ Series of InstrumentsRUO-IDV-05-2095-A8 of 1811 Operational Precautions andLimitations Safety: AS/NZ 61010-1 and IEC 61010-2-061 Canada Electromagnetic Interference (EMI): CAN/CSAA CISPR11.

9 This ISM device complies with CanadianICES-001. Safety: CAN/CSA No. 61010-1 and CAN/CSA No 61010-2-061 Europe Electromagnetic Compatibility (EMC): Electromagnetic Compatibility directive 2004/108/EC asimplemented in these standards: EN 61326-1 EN 55011 (Class A) Safety: Low Voltage Directives 2006/95/EC as implemented in these standards: EN 61010-1 EN 61010-2-061 Waste Electrical and Electronic Equipment (WEEE): Waste Electrical and Electronic Equipment2012/96/EEC, as implemented in EN 40519 Packaging and Packaging Waste (PPW): Packaging and Packaging Waste Directive 94/62/ECUnited States Radio Emissions Interference Regulations: 47 CFR 15 as implemented in this standard: FCC Part 15(Class A) Safety: Occupational Safety and Health Regulations, 29 CFR 1910, as implemented by the following standards.

10 UL 61010-1 IEC 61010-2-0616500 and 6500+ Series of InstrumentsSystem User Guide9 of 181 RUO-IDV-05-2095-AOperational Precautions and LimitationsInternational Electromagnetic Compatibility (EMC): IEC 61326-1 IEC CISPR 11 (Class A) IEC 61000-3-2 IEC 61000-3-3 Safety: IEC 61010-1 IEC 61010-2-061 Electrical PrecautionsWARNING! Electrical Shock Hazard. Do not remove the covers. Removing the coversmight cause injury or malfunctioning of the System . The covers need not be removedfor routine maintenance, inspection, or adjustment. Contact the Sciex FSE for repairsthat require the covers to be information on System electrical specifications, refer to the Site Planning Mains SupplyWARNING! Electrical Shock Hazard. Use only qualified personnel for the installationof all electrical supplies and fixtures, and make sure that all installations adhere tolocal regulations and safety !