October 6, 2016 Page 1 All part IIs, graduate students & postdocs welcome. 8 lectures in Michaelmas term, Wolfson seminar room 11am, Thursdays. 1. Oct 13 th Introduction to mass spectrometry and basic principles 2. Oct 20 th Mass Analysers: Quadrupoles, Time of Flight, Orbitraps and hybrid instruments. 3. Oct 27 th Collisions in vacuum: cooling, activating, and sizing ions. 4. Nov 3 rd Ion Chemistry in mass spectrometry 5. Nov 10 th Separation methods (chromatography) coupled to mass spectrometry. 6. Nov 17 th Proteomics break 7. Dec 1 st Metabolomics 8. Dec 8 th Mass spectrometry for biophysics and structural biology. Graduate Course in Mass Spectrometry starting 13th Oct.
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October 6, 2016Page 1
Graduate course in mass spectrometry starting 13th Oct.
All part IIs, graduate students & postdocs welcome.
8 lectures in Michaelmas term, Wolfson seminar room 11am, Thursdays.
1. Oct 13th Introduction to mass spectrometry and basic principles2. Oct 20th Mass Analysers: Quadrupoles, Time of Flight, Orbitraps and hybrid instruments.3. Oct 27th Collisions in vacuum: cooling, activating, and sizing ions. 4. Nov 3rd Ion Chemistry in mass spectrometry 5. Nov 10th Separation methods (chromatography) coupled to mass spectrometry. 6. Nov 17th Proteomics break7. Dec 1st Metabolomics8. Dec 8th Mass spectrometry for biophysics and structural biology.
Graduate Course in Mass Spectrometry starting 13th Oct.
DEPARTMENT OF CHEMISTRYMASS SPECTROMETRY RESEARCH FACILITY
Professor James McCullagh, Head of the Mass Spectrometry Research Facility
INTRODUCTION TO THE CRL MASS SPECTROMETRY RESEARCH FACILITY
Introduction
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
1. MS overview2. People3. Facilities4. Instrument locations5. Open access MS6. Trained users MS7. Project work8. Software and data storage9. Lectures and events
Identification Chemical formula prediction
260.0297185↓
C6H13O9P↓
Glucose-1-phosphate
What can mass spectrometry do for you?
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Structural analysisFragmentation studies using MS
Quantification Relative or absolute
LC/MS, GC/MS
Different types of MSInlets, ionisation, sensitivity accuracy
People in the Mass Spectrometry Research Facility
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Prof James McCullaghHead of Research facility
Dr James WickensMS Services Manager Research Associate
Ms Elisabete PiresResearch Associate
22 MS systems4 full time staffMultiple services
Dr Ashley ShepherdResearch Associate
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MS facility and staff support Research in the CRL (Part II, DPhil, Postdoc and PIs).
Location of main MS labs in CRL
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Basement Mass Spec Lab 2
Basement Mass Spec Lab 1
Types of access to mass spectrometry
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
1. OPEN ACCESS MASS SPECTROMTRY walk up Instruments on ground floor (initial registration and training 10 mins.) anyone in Chemistry Department can use.
2. MASS SPECTROMETRY SUBMISSION SERVICES Accurate Mass Service (Lecture on this will be held in CRL in Oct)Alternative ionisation MS Proteomics service.Special samples – we can often help with samples which fall outside the remit above – please come and talk to a member of staff.
Dr James Wickens Mass Spectrometry
Services Manager
Types of access to mass spectrometry
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Dr James Wickens Mass Spectrometry
Services Manager
3. TRAINED USER INSTRUMENTS 9 instruments – require training course – can then book and use whenever you like. Open to all but please email or come and see James Wickens or James McCullagh to discuss needs first. LC/MS, GC/MS and MALDI available.
4. RESEARCH COLLABORATIONSMethod development for bespoke systemsProteomics and post-translations modifications analysisMetabolite identification
1. Open Access Mass Spectrometry
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
SMALL MOLECULES (100-2000 Da)1. Runs 60,000 samples/yr2. 2 mins per sample3. Used almost continuously4. 10min familiarisation training Mon/Tue/Wed5. Sign up sheet required after NMR lecture.
PROTEIN OPEN ACCESS1. Fast column chromatography LC/MS2. 10mins per sample3. Fewer users – see a member of MS staff
for training
OPEN ACCESS LC/MS1. Fast column chromatography LC/MS2. <10mins per sample
Small molecule open access
Protein open access
Ground floor MS room
Ground floor MS room
1. Open access results
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Small molecule open access Protein open access
Small moleculesResults are emailed as a PDFRaw data files available from3am next day on the chemistrynetwork: \\FILES-SUPPORT\Mass Spectrometry\Open Access
Protein Open AccessResults deposited as PDF in sepárate folder in same location.
Results: PDF emailed Results: PDF emailed
Adducts M+HM+NaM-H
1. Location of open access systems: ground floor CRL
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
All open access MS systems are located in the ground MS room
2. Small molecule characterisation services
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
SMALL MOLECULES (ORGANIC AND INORGANIC COMPOUNDS):1. Accurate Mass Service (novel compounds)2. High resolution Service (unable to obtain results by open access)
Small molecules sample login: Ground floor Lab 20.062 (same as open access)
Dr James Wickens Mass Spectrometry Services Manager
2. Sample submission
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
White excel spreadsheet:‘Alternative ionisation service’
Yellow spreadsheet: ‘Accurate Mass service’1. 2.
1. Obtain an MSS or ESI number from sample login computer in ground floor open access MS room
2. Complete white sample submission form including your new MSS or ESI number (the form can be found under MS services on the MS website)
3. Label sample vial with MSS number or ESI number
4. Place labelled samples in tray in sample submission fridge
4. 3.
All results will be emailed to the email address provided on the submission form. Forms filled out incorrectly will not be processed.
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Q-TOF: Equipped with nano-ESI source robot (AdvionNanomate). Useful for analysis of native state proteins (with tertiary structure intact) and protein complexes.
Waters Q‐TOF Micro
• Native state protein ID• PTM analysis• Binding assays
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Waters MALDI micro
Matrix-Assisted Laser-Desorption Ionisation (MALDI) isa laser based ionisationtechnique useful for identificationof:
• Peptides/proteins• Oligonucleotides• Polymers. • Small molecules above 450 Da.
AB Sciex MALDI TOF-TOF
3. Trained user instrument access
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
1. Discuss and agree training is necessary with your supervisor.
2. Email or come and see James McCullagh or James Wickens who will arrange the training which takes 2-3 hours.
3. Once completed you will be able to book and use the instrument unsupervised.
4. You may not use any trained user instruments unless you have received training from a member of the MS staff.
4. Other instruments
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
4.OtherExperiments
Orbitrap Exactive Plus
Stable isotope ratio mass spectrometry
Inert atmosphere MS
SYNAPT ion mobility MS
Probe MS Orbitrap Q‐Exactive
Areas of focus within the MS facility team
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Prof James McCullaghHead of Research facility
Dr James WickensMS Services Manager
New person Research Associate
Ms Elisabete PiresResearch Associate
Dr Ashley ShepherdResearch Associate
Areas of focusGCGC/MSMS of SolidsMALDIInorganic analysis
Areas of focusProteomicsMetabolomicsBiological MSLC/MSMALDISample prep
Areas of focusGCGC/MSMALDIAccurate Mass Analysis
Areas of focusGC/MSLC/MSOpen accessProbe MSOrbitrap MSSample prep
Areas of focusLC/MSMetabolomicsIsotope tracersIRMSIC-MSOrbitrap MSSample prep
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Mass Spectrometry Data Files: MassStore
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
MS experiments, particularly LC/MS and GC/MS create large data files. A typical proteomics data file for example can be > 200GB per sample.
\\FILES-SUPPORT\Mass Spectrometry\MassStore-Research Groups
MS and NMR Software: Mestrenova
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Mestrenova software is available for download from the Mass Spectrometry and NMR websites. This can be used to interrogate MS and NMR data, transform and collate for presentations. See MS website for further details about how to download.
• Accurate Mass analysis• Identify LC/MS peaks• Interrogate open access results• Collate NMR and MS data
together• Annotate spectra• Produce reports
Protocols and Safety in the MS labs
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
1. No lab coats to be worn in any of the MS labs.
3. Open access data is backed up and stored for a period of 5 years. If you need
access to these data files please see a member of MS staff.
2. Never remove or modify any part of the mass spectrometer system, sample inlet
system or software. If something is not working properly please report to a member
of the MS facility staff.
4. Please read safety information on the mass spectrometry website and all
information provided at Mass Spectrometer terminals.
Mass Spectrometry Facility Website
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Training courses and Lectures in MS
Mass Spectrometry website: http://www.chem.ox.ac.uk/spectroscopy/mass-spec/
Open access Training (Organic NMR and Mass Spectrometry):Sign up sheets at end of NMR talkThursday 6th and Friday 7th
Open Access Training for Inorganic users Monday 10th sign up sheet other side of desk
Large molecule/protein open access training Please contact Elisabete Pires in the first instance (MS services Manager) to arrange training. [email protected]
Graduate Lecture Course in Mass Spectrometry(see website for schedule (8 lectures starting October 13th 2016).