Mass Spectrometry Center
University of Washington * School of Pharmacy
Department of Medicinal Chemistry

Instrument	Year	Ionization Source(s) & Mass Analyzer Type(s)	General Applications	Image
Waters Micromass Quattro Micro API MassLynx 4.1 WIndows XP OS	2008	± ESI & APCI (QHQ)MS/MS Tandem Quadrupole MS	Automated LC/MS/MS quantification. Drug metabolism studies. Analysis of complex biological extracts.
Waters Micromass Quattro Premier XE MassLynx 4.1 Windows XP OS	2006	± ESI & APCI (QTQ)MS/MS Tandem Quadrupole MS	Automated LC/MS/MS quantification. Drug metabolism studies. Analysis of complex biological extracts.
Shimadzu QP2010 GCMS Solutions 2.21 Windows XP OS	2006	± EI & CI (Q)MS Quadrupole MS	Automated GC/MS quantitative and qualitative analysis. Drugs, metabolites, synthetic and natural products.
Thermo LTQ-OT* Xcalibur 2.0 Windows XP OS	2006	± ESI LTQ Orbitrap MS/MS Fourier transform Tandem Hybrid MS	Capillary LC/MS/MS of proteolytic digests of simple and complex mixtures.
Thermo LTQ-FT* Xcalibur 2.0 Windows XP OS	2004	± ESI LTQ [FT(ICR)] MS/MS Fourier transform Tandem Hybrid MS	Capillary LC/MS/MS of proteolytic digests of simple and complex mixtures.
Bruker AutoFlex II Compass 1.0 WIndows 2000 OS	2004	± MALDI TOF MS Time of Flight MS	Characterization and identification of proteins by peptide mass mapping. PSD peptide sequencing.
Waters Micromass Platform LCZ MassLynx 4.0 WIndows XP OS	2004	± ESI & APCI (Q)MS Quadrupole MS	Fully automated quantitative analysis of drugs and metabolites.
Bruker APEX Qe 47 APEX Control 2.0.0.36 Windows XP OS	2002	± ESI QH [FT(ICR)] MS/MS Fourier transform Tandem Hybrid MS	Identification & quantification of sample limited biologic materials by combined high resolution mass accuracy & high sensitivity.
Agilent Technologies LC/MSD/ChemStation Windows XP OS	1999	± ESI & APCI (Q)MS Quadrupole MS	Fully automated quantitative analysis of drugs and metabolites.
*Goodlett Laboratory Proteomic Core instrumentation operated within the Center.

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Waters Micromass Quattro Micro API: Tandem Quadrupole Mass Spectrometer (QHQ) MS/MS
Manufacturer:	Waters Corporation, Milford, MA, USA
*Mass range:	2000 Dalton (Primary & Secondary Beams)
*Resolution:	Unit mass (Q1 & Q2)
Interface:	Micromass Zspray™ Atmospheric Pressure Ionization (API) Source
Ionization (±eV):	Electrospray & Atmospheric Pressure chemical Ionization (ESI & ApcI)
*Ion Detection :	Daly detector after Q2
Inlet Systems:	Liquid Chromatograph (LC): Shimadzu LC-10AD Pumps (2) with SPD-10AV UV-Vis Variable Detector (Shimadzu Scientific Instruments, Inc., Columbia, MD) Split: Variable Infusion: Harvard Apparatus Model 22 Syringe infusion pump (Harvard Apparatus, Inc., South Natick, MA) Loop/Flow Injection Analysis (FIA) LC solvent delivery (10 - 1000ul min.-1) with sample injection Sampling System: Shimadzu SIL-10ADVP Auto Injector (Shimadzu Scientific Instruments, Inc., Columbia, MD) Rheodyne 8125 or 7125 Manual Injectors (Rheodyne Inc., Cotati, CA -- now part of Idex Health & Science Group)
Data System (DS):	Hardware: Lenovo Pentium 4, 1.86 GHz, 1Gbyte RAM Software: Microsoft Windows XP, Micromass MassLynx® 4.1, MaxEnt® & BioLynx®
Acquisition Date:	2008
Funding:	Drug Metabolism, Transport and Pharmacogenomic Research (DMTPR) Fund Pharmacia, Inc. (Gift)
Predominant Uses:	Drug, metabolite & conjugate studies (qualitative & automated quantification); tandem MS analysis of non-volatile and thermally-labile complex biological extracts and biopolymers; intact protein purity and mass determination.
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Waters Micromass Quattro Premier XE Tandem Quadrupole Mass Spectrometer (QT™Q)MS/MS
Manufacturer:	Waters Corporation, Milford, MA, USA
Mass range:	3000 Dalton (Primary & Secondary Beams)
Resolution:	Unit mass (Q1 & Q2)
Collision Cell:	T-wave™(T) - rf traveling wave technology
Interface:	Micromass Zspray™ Atmospheric Pressure Ionization (API) Source
Ionization (±eV):	Electrospray & Atmospheric Pressure chemical Ionization (ESI & APCI) Atmospheric Pressure Photo Ionization (APPI)
Ion Detection :	Daly detector after Q2
Inlet Systems:	Liquid Chromatograph (LC): Waters ACQUITY Ultra Performance LC™ (UPLC™) System (Waters Corp., Milford, MA) Infusion: Integral syringe pump solvent delivery system (1 - 1000 ul min.-1) Sampling System: Autoinjector integral to the Waters ACQUITY UPLC™ System
Data System:	Hardware: IBM Pentium 4, 3.2 GHz, 1 Gbyte RAM Software: Microsoft Windows XP, Micromass MassLynx® 4.1
Acquisition Date:	2006
Funding:	Mass Spectrometry Center Equipment Budget Office of the Dean of the School of Pharmacy *Drug Metabolism, Transport, and Pharmacogenomic Research (DMTPR) Fund Department of Medicine/Metabolism, Endocrinology, Nutrition
Predominant Uses:	Drug, metabolite & conjugate studies (qualitative & automated quantification); tandem MS analysis of non-volatile and thermally-labile complex biological extracts *and biopolymers; protein purity and mass determinations.
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Shimadzu QP2010 Gas Chromatograph Quadrupole Mass Spectrometer (GC-QMS)
Manufacturer:	Shimadzu Scientific Instruments, Columbia, MD
Mass range:	1.5 - 1024 Dalton
Resolution:	Unit mass
Ionization (±eV):	Electron, Chemical Ionization (EI, CI & NCI)
Inlet Systems:	Gas Chromatograph (GC): Shimadzu GC-2010 ( Shimadzu Scientific Instruments, Columbia, MD) Injectors: Capillary split-splitless Sampling System: Shimadzu AOC-20i Auto Injector DI-2010 Direct Insertion Probe (Shimadzu Scientific Instruments, Columbia, MD)
Data System:	Hardware: MPC, Pentium 4, 3.2 GHz, 1GB RAM Software: Microsoft Windows XP, Shimadzu GCMS Solutions
Acquisition Date:	2005
Funding:	Mass Spectrometry Center Equipment Budget
Predominant Uses:	Automated quantitative metabolic profiling in drug metabolism and drug interaction studies and the qualitative analysis of synthetic and natural products.
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Thermo Linear Trap Quadrupole Fourier transform (Orbitrap) Mass Spectrometer LTQ-OT MS/MS
Manufacturer:	Thermo Electron Corp., San Jose, CA, USA
Mass range:	≤ 2000 & 4000 Dalton (normal and extended modes, respectively)
Resolution:	Unit mass (LTQ MS) ≤ 100,000 (FWHM)* at m/z 400, typically 60,000 (OT MS)
Ionization (±eV):	Electrospray Ionization (ESI)
Ion Detection:	Electron multipliers (LTQ MS) Fourier transform image current (OT MS)
Inlet Systems:	Liquid Chromatograph (LC): Waters nanoACQUITY Ultra Performance LC™ (UPLC™) System ( Waters Corp., Milford, MA) Infusion: Integral syringe pump solvent delivery (100nl - 2000nl min.-1) Loop/Flow Injection Analysis (FIA): LC solvent delivery (0.01ml – 40.00ul min.-1) with sample injection Syringe pump solvent delivery (100nl - 2000nl min.-1) with sample injection
Sampling System:	Autoinjector integral to the Waters nanoACQUITY UPLC™ System Valco CI4W sample injector (1ul internal loop) (Valco Instruments Co., Houston, TX)
Data System:	Hardware: Dell Optiplex GX52, Pentium 4, 3.2GHz, 1 Gbyte RAM Software: Microsoft Windows XP Professional, Excalibur 2.0 SR1™, Magic AutoSampler 2.0 & Paradigm MS4 2.0
Acquisition Date:	2006
Funding:	The National Institutes of Health (NIH): NCRR 1 S10 RR17262-01 award entitled: “Fourier transforms-ion cyclotron-resonance mass spectrometer”
Predominant Uses:	Automated “shotgun” proteomic analysis - Combining nano-LC, data dependent MS/MS with high sensitivity (sub fmol on-column) and accurate mass measurement (2 ppm) for protein identifications in simple and complex protein mixtures. LC/MS/MS, label-free quantification, and accurate mass measurements.
	*FWHM = full width at half height
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Thermo Linear Trap Quadrupole Fourier transform (Ion Cyclotron Resonance) Mass Spectrometer LTQ-FT MS/MS
Manufacturer:	Thermo Electron Corp., San Jose, CA, USA
Magnet:	actively shielded 7.0 Tesla superconducting
Mass range:	≤ 2000 Da (normal mode), 4000 Da (extended mode)
Resolution:	Unit mass (LTQ MS) ≤ 500,000 (FWHM)* at m/z 400, typically 100,000 [FT(ICR) MS]
Ionization (±eV):	Electrospray Ionization (ESI)
Inlet Systems:	Liquid Chromatograph (LC): Michrom MS4B multi-Dimensional Separations module (Michrom BioResources, Auburn, CA) Infusion: Harvard Apparatus PHD 22/2000 syringe pump (Harvard Apparatus, Inc., Holliston, MA) Nanospray vai metal coated glass capillary (New Objective, Inc., Woburn, MA)
Sampling System:	MIchrom Endurance Bio-Cool Paradigm AS1 Autosampler (Michrom BioResources, Inc.)
Data System:	Hardware: Dell Optiplex GX270, Pentium 4, 2.8GHz, 1 Gbyte RAM Software: Microsoft Windows XP Professional, Excalibur 2.0 SR1™, LTQ-FT MS 2.0 RC6, Magic AutoSampler 2.0 & Paradigm MS4 2.0
Acquisition Date:	2004
Funding:	The National Institutes of Health (NIH): NCRR 1 S10 RR17262-01 award entitled: "Fourier transforms-ion cyclotron-resonance mass spectrometer"
Predominant Uses:	Automated “shotgun” proteomic analysis - Combining nano-LC, data dependent MS/MS with high sensitivity (sub fmol on-column) and accurate mass measurement (2 ppm) for protein identifications in simple and complex protein mixtures. LC/MS/MS, label-free quantification, and accurate mass measurements.
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Bruker AutoFlex II Matrix-Assisted LASER Desorption Ionization - Time of Flight Mass Spectrometer (MALDI-TOF)MS
Manufacturer:	Bruker Daltonics, Billerica, MA, USA
Mass range:	Linear: > 132kDa [Bovine Albumin (2MH+)] Reflectron: > 6,000 Da
Resolution:	Linear: > 4,000 (FWHM)* @ m/z 2,465.2 [ACTH (18-39)] Reflectron: > 18,000 (FWHM)* @ m/z 3,147 (Somatostatin)
Sensitivity:	Linear: S/N>10:1 for 1 fmole at m/z 1,570.68 (Glu-Fib) Reflectron: S/N>10:1 for 1 fmole at m/z 1,570.68 (Glu-Fib)
Mass Accuracy:	Linear: < 100 ppm Reflectron: < 10 ppm
Ionization (±eV):	Matrix Assisted LASER Desorption (MALDI) - 337 nm Nitrogen laser
Detectors:	Two Micro Channel Plates (MCP), Linear and Reflectron, 2 GHz time-to-digital converter (TDC)
Inlet Systems:	SCOUT MTP Microtiter Plate Ion Source with Observation Optics
Data System:	Hardware: HP workstation XW 6000, 2 GHz dual-Xeon processor, 1GByte RAM Software: Microsoft Windows 2000 (v5.0); Bruker Compass 1.0, FlexControl and Flex Analysis 2.0 and license, ClinProTools 2.0 GUI Integrated vacuum measurement and control unit
Acquisition Date:	2004
Funding:	Departments of Biochemistry, Chemistry, Medicinal Chemistry, Periodontics and Oral Biology, Medicine (Infectious Diseases) Center for Ecogenetics and Environmental Health (CEEH) School of Pharmacy and its Drug Metabolism/Transport & Pharmacogenomics Research Program (DMTPR) University of Washington Mass Spectrometry Center
Predominant Uses:	Characterization of biopolymers (proteins, protein digests and oligonucleotides); peptide sequencing using post source decay (PSD) techniques.
	*FWHM = full width at half height
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Waters Micromass Platform LCZ: Quadrupole Mass Spectrometer QMS
Manufacturer:	Waters Corporation, Milford, MA, USA
Mass range:	3000 Dalton
Resolution:	Unit mass
Interface:	Micromass Zspray™ Atmospheric Pressure Ionization (API) Source
Ionization (±eV):	Electrospray & Atmospheric Pressure chemical Ionization (ESI & APcI)
Inlet Systems:	Liquid Chromatograph (LC): Shimadzu LC-10AD Pumps (2) (Shimadzu Scientific Instruments, Inc., Columbia, MD) Split: Variable Infusion: Harvard Apparatus Model 22 Syringe infusion pump (Harvard Apparatus, Inc., South Natick, MA) Loop/Flow Injection Analysis (FIA) LC solvent delivery (10 - 1000ul min.-1) with sample injection Sampling System: Shimadzu SIL-10ADVP Auto Injector (Shimadzu Scientific Instruments, Inc., Columbia, MD) Rheodyne 8125 or 7125 Manual Injectors (Rheodyne Inc., Cotati, CA -- now part of Idex Health & Science Group)
Data System:	Hardware: 1GHz Pentium III processor, 512 MB RAM Software: Microsoft Windows XP, MassLynx® 4.0, MaxEnt® & BioLynx®
Acquisition Date:	2004
Funding:	Amgen nc. - Gift (July 2004) Mass Spectrometry Center Equipment Budget
Predominant Uses:	Fully automated quantitative analysis of drugs and metabolites.
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Bruker APEX Qe 47e: Fourier transform (Ion Cyclotron Resonance) Mass Spectrometer [FT(ICR)]MS
Manufacturer:	Bruker Daltonics, Billerica, MA, USA
Magnet:	160mm bore actively shielded 4.7 Tesla superconducting (Magnex Scientific Ltd., Oxford, UK)
Mass range:	> 66kDa (BSA specification)
Resolution:	> 450,000 (FWHM)*
Ionization (±eV):	Electrospray Ionization (ESI)
Inlet Systems:	Infusion: Cole Parmer Series 74900 Syringe pump (Cole Parmer Instrument Co., Vernon Hills, IL) Loop/Flow Injection Analysis (FIA) Syringe pump solvent delivery with Valco CI4W sample injector (500nl internal loop) (Valco Instruments Co., Houston, TX) Apollo Nanoflow Electrospray Ionization Source
Data System:	Hardware: Dell WHL 1.7 GHz Xeon CPU, 1.5 GByte memory Software: Microsoft Windows XP, Hummingbird Exceed PC X Server, Bruker APEX Control 2.0.0.36 Bruker BioTools and RapiDeNovo™(2.2)
Acquisition Date:	2002
Funding:	Mass Spectrometry Center Equipment Budget University of Washington Pharmacia (Gift) Merck Research Laboratories (Gift) Weyerhaeuser Company (Gift) The National Institutes of Health (NIH)
Upgrades:	QH-hybrid front end upgrade with CID, ECD, IRMPD, DREAMS and reduced noise detection system and X-Y-Z Nanospray positioning (2006)
Predominant Uses:	Application of combined high resolution, high accuracy mass measurement and high sensitivity to the detection, identification and quantification of sample limited biologic materials.
	*FWHM = full width at half height
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Agilent Technologies LC/MSD Series 1100: Quadrupole Mass Spectrometer (QMS)
Manufacturer:	Agilent Technologies, Palo Alto, CA
Mass range:	3000 Dalton
Resolution:	Unit mass
API Interface:	Orthogonal Spray Ionization Source
Ionization (±eV):	Electrospray (ES) & Atmospheric Pressure Chemical Ionization (APcI)
Inlet Systems:	Liquid Chromatograph (LC): Agilent Technologies Series 1100 binary solvent delivery system Series 1100 UV-VIS Diode Array Detector (DAD) ( Agilent Technologies, Palo Alto, CA)
Sampling System:	Agilent Technologies 1100 Well-Plate Autosampler
Data System:	Hardware: Dell Dimension 5100C Pentium 4, 3GHz CPU, 1 Gbyte RAM Software: Microsoft Windows XP, LC/MSD ChemStation 10.02 (rev A)
Acquisition Date:	1999
Funding:	Mass Spectrometry Center Equipment Budget University of Washington
Upgrades:	LAN control, High Performance and Autosampler (2004) Dell 5100C and Windows XP (2006)
Predominant Uses:	Fully automated quantitative analyses
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Instruments | Services | Contacts | Rates Sample Submission | Links | Home Department of Medicinal Chemistry School of Pharmacy | University of Washington   For more information about the Mass Spectrometry Center, contact Dale Whittington. For comments or suggestions on this web site, contact Caryl Lynch. Last updated: April 6, 2009