Mass Spectrometry / Microanalysis
About
Mass Spectrometry Facility at UBC Chemistry Department is equipped with modern analytical instrumentation, providing most of the mass spectrometric techniques currently available.
Contact Information
Yun Ling, Ph. D.
Department of Chemistry
University of British Columbia
2036 Main Mall
Vancouver, BC V6T 1Z1
Canada
Tel: 604-822-3235 (office)
604-827-4212 (lab)
Fax: 604-822-2847
Email:
Location
Laboratory: E313/E315
Lab Phone No. 604-8274212
Department of Chemistry
University of British Columbia
2036 Main Mall
Vancouver, BC V6T 1Z1
Canada
Staff
Yun Ling, Ph.D. Facility Manager
Jenny Lai, Research Technician
Jane Zhu, Research Technician
Larry Hua, Research Technician
Instruments
Waters LCMS (ZQ)
This LCMS system, installed in 2004, consists of Water ZQ equipped with ESCI ion source and 2695 HPLC. It is mainly used for routine molecular mass determination of polar organic compounds. The system is set up as a walk-up LCMS or so-called OAMS (open access MS). It is available to researchers in the Chemistry Department for self-service.
Waters LCMS (SQ-D2)
This LCMS system, installed in 2023 to replace the old Waters LCMS, consists of Waters SQ Detector 2 (SQ D2) equipped with ESCI ion source and Waters Arc HPLC. It is mainly used for routine molecular mass determination of polar organic compounds. The system is set up as a walk-up LCMS or so-called OAMS (open access MS). It is available to researchers in the Chemistry Department for self-service.
Bruker HCT
The name of this mass spectrometer is Bruker HCTultra PTM. Installed in 2014, HCT is a Bruker ion trap mass spectrometer equipped with electrospray (ESI) ion source. Agilent 1100 HPLC is coupled for LC-MS analysis. Sample could be introduced by infusion, flow-injection or on-line HPLC. The HCT has mass range of up to 3,000. MS/MS for ESI samples can be measured on this instrument. The instrument is available to researchers in the Chemistry Department for self-service.
Bruker autoflex
The name of this instrument is Bruker autoflex speed LRF MALDI-TOF. It was installed in 2012. This is a time-of-flight (TOF) mass spectrometer equipped with MALDI ion source. Laser is a 1 KHz smartbeam-II laser with wavelength of 355 nm. The autoflex speed LRF can be operated in either linear or reflectron mode. Mass range in linear mode can be as high as 100KDa. Mass accuracy in linear mode is around 0.1%. Mass resolving power in the reflectron mode can be as high as 26,000. Mass accuracy in the reflectron mode is typically 0.01%. It is mainly used for routine molecular mass determination of orgamometallics, supramolecular coordination assemblies, synthetic polymers, and biomolecules. The system is available to researchers in the Chemistry Department for self-service,
Agilent GCMS
This GCMS, installed in 2015, consists of Agilent 5977A MSD and 7890B GC. The MSD is a single quad mass analyzer with mass range of up to 1,050. Both EI and CI source are available. EI is normally installed. The GC is equipped with the split/splitless (S/SL) inlet and a multimode inlet (MMI). A thermal separation probe (TSP) can be installed on the MMI inlet for direct sample introduction without separation. This GCMS is mainly used for routine molecular mass determination of non-polar organic compounds. The system is available to researchers in the Chemistry Department for self-service.
Jeol GCTOF
The name of this instrument is Jeol JMS-T100GCV AccuTOF GCv 4G. It was installed in 2018. This is a time-of-flight (TOF) mass spectrometer coupled to GC (GCTOF). It is equipped with multiple ion sources including electron ionization (EI), chemical ionization (CI) and field desorption/field ionization (FD/FI) ion source. FD source is normally installed. The GC is an Agilent 7890B. This system provides us the capability of analyzing wide range of compounds (polar and non-polar) due to different ionization methods available and extended mass range (up to 5000) due to TOF MS analyzer. The TOF is capable of delivering mass resolving power of 8,000 and mass accuracy of 4ppm. Sample can be introduced using different probes including direct insertion probe (DIP) for EI or CI, FD probe and LIFDI probe, as well as GC. LIFDI probe is used for mass analysis of air-sensitive compounds.
Agilent QTOF
The name of this mass spectrometer is Agilent 6545 QTOF. Installed in 2019, it is a high resolution tandem mass spectrometer coupled with Agilent 1260 infinity II HPLC system. Both electrospray (ESI, Agilent JetStream) and atmospheric pressure chemical ionization (APCI) ion source are available. ESI is preferred for polar structures and APCI for less polar structures. ESI source is normally installed. The 6545 QTOF has resolving power of >40,000 and mass accuracy of <1ppm in MS mode and <2ppm in MS/MS mode. Mass range is up to 10,000 in extended mass range mode, or up to 3,200 for typical operations. Samples could be introduced by flow-injection or on-line HPLC. This system can be used for low resolution analysis for nominal mass confirmation, high resolution accurate mass measurements for elemental composition determination of polar compounds and tandem mass spectrometry analysis for structure elucidation and LC-MS analysis of reaction mixtures.
Thermo LTQ-Orbitrap
This instrument was moved from UBC Faculty of Dentistry, Centre for High High-Throughput Phenogenomics, to our lab in 2020. This is a LTQ Orbitrap XL equipped with a MALDI ion source. LTQ-Orbitrap is a high resolution tandem mass spectrometer. Laser on this system is a nitrogen laser with wavelength of 337 nm. This instrument has mass range of up to 4,000, mass resolving power of up to 100,000. It can be used for MALDI-MS or MALDI-MS/MS experiments. It can also be used for MS imaging.
Thermo Quantis TSQ
The name of the mass spectrometer is Thermo TSQ Quantis and HPLC is Vanquish UHPLC. It was installed in 2021. TSQ quantis is a triple quadrupole mass spectrometer. Both electrospray (ESI) and atmospheric pressure chemical ionization (APCI) ion source are available. ESI is preferred for polar structures and APCI for less polar structures. ESI source is normally installed. It has a mass range of up to 3,000. It can be used for quantitative analysis of small molecules.
Thermo Flash 2000 EA
The name of this instrument is Thermo Flash 2000 Elemental Analyzer. It was installed in 2015. This instrument can be used for the determination of total carbon, hydrogen, nitrogen, and sulphur (C, H, N, S) present in a wide range of organic and organometallics samples.
Services
Services available
Sample submission
Training and booking for self-serve mass spec
Services Available
Sample should be submitted online at https://xenon.chem.ubc.ca/ms-ea/index.php/
Mass Spectrometry Services
|
Services |
Instruments |
Compounds |
|
EI (Electron Impact Ionization) - low and high res |
Agilent GCMS Jeol GCTOF |
Non-polar Organic |
|
CI (Chemical Ionization) – low and high res |
Agilent GCMS Jeol GCTOF |
Polar Organic |
|
FD/FI (Field Desorption/Field Ionization) - low and high res |
Jeol GCTOF |
Non-polar or polar organic, Organometallics, Coordination compounds, |
|
LIFDI (Liquid-Injection Field Desorption Ionization)-low res |
Jeol GCTOF |
Air-sensitive compounds |
|
ESI (Electrospray Ionization) - low and high res |
Bruker HCT Waters LCMS |
Polar Organic, Organometallics, Coordination compounds, Bio-organic |
|
APCI (Atmospheric Pressure Chemical Ionization)- low and high res |
Agilent QTOF |
Less polar organic, Coordination Compounds, Organometallics |
|
MALDI (Matrix-Assisted Laser Desorption/Ionization) |
Bruker autoflex Thermo LTQ-Orbitrap |
Coordination compounds Organometallics, Supramolecular complexes, Bio-organic, Synthetic Polymers |
| MS/MS (ESI, APCI or MALDI) |
Bruker HCT Agilent QTOF Thermo Quantis Thermo LTQ-Orbitrap
|
Polar Organic Coordination compounds Organometallics Bio-organic |
|
LC-MS (Liquid Chromatography-Mass Spectrometry) |
Bruker HCT coupled with Agilent 1100LC Agilent QTOF coupled with 1200 LC Thermo Quantis TSQ coupled with Vanquish UHPLC |
Mixture of polar organic compounds |
|
GC-MS (Gas Chromatography- Mass Spectrometry)
|
Agilent GCMS | Mixture of non-polar Organic compounds |
|
MALDI MS Imaging
|
Thermo LTQ-Orbitrap |
*Air-sensitive sample is run on Jeol GCTOF with FD source and sample is introduced by using LIFDI probe.
Low res MS services normally refer to full scan MS and provide nominal mass measurements. They are currently available for EI, ESI, APCI, MALDI, FD and LIFDI. A molecular mass measurement (nominal or average mass) can be used to determine the molecular weight of a compound, confirming the presence or absence of a compound. For some low res MS services, multiple instruments can be used.
High res MS services are generally referred to as accurate mass measurement on the mass of interest normally performed on high resolution mass spectrometer to generate possible elemental compositions. Low res MS needs to be performed first and the mass to be measured must be confirmed in low res full scan. They are available for some ionization modes (EI, FD, ESI, and APCI).
MS/MS analyses are available for ESI, APCI and MALDI ions. MS/MS spectra could be used to provide structure information of a compound. Low res full scan MS should be performed and the mass that MS/MS to be performed on must be confirmed before submitting for MS/MS.
GC-MS is used for analysis of non-polar organic compound mixture. Both EI and CI are available, but EI is normally installed. The analysis could be qualitative, or quantitative.
LC-MS can be used for analysis of polar organic compound mixture. Both ESI and APCI are available, but ESI is normally installed. The analysis could be qualitative, or quantitative.
Imaging MS
Elemental Analysis Service
Our elemental analysis is organic elemental analysis (OEA). It is used to determine the elemental compositions of organic compounds. CHN and CHNS determinations are available. The analysis can be used to verify a formula or purity of a compound.
Sample Submission
Sample should be submitted online at https://xenon.chem.ubc.ca/ms-ea/index.php/
Electron Impact Ionization (EI)- low res and high res
Samples submitted for EI analysis can be analyzed on Agilent GCMS, or Jeol GCTOF. Sample should be submitted as solid or neat liquid. Non-polar solvent should be used if submitted in solution. Samples submitted for high resolution EI analysis will be first analyzed by low resolution EI to determine if the mass to be measured for the expected compound is found. Or users are asked to provide a low resolution EI MS. High res accurate mass can be measured on Jeol GCTOF.
Please note that non-polar organic compounds that work with EI should also work with FD. Please submit for FD instead because FD source is normally installed on the GCTOF unless high res EI is absolutely needed.
Chemical Ionization (CI) – low and high res (N/A currently)
Please note that compounds that work with CI should work with APCI, FD or even ESI. Since CI source is normally not installed on Agilent GCMS, or Jeol GCTOF, you should consider FD or ESI unless CI is absolutely needed. Please contact the facility manager if CI is absolutely needed.
Field Desorption and Ionization (FD/FI) – low and high res
Samples submitted for FD MS will be analyzed on Jeol GCTOF. Solid samples are preferred. If submitted in solution, the concentration should be 0.1 -1mg/mL. Solvents can be either polar or non-polar organic solvent, but should be low boiling point (bp) because solvent needs to be volatile enough to evaporate prior to introduction of the probe into the vacuum lock. Avoid using pure water and metal salts, or buffer.
Liquid Injection Field Desorption Ionization (LIFDI)
Samples can be only submitted in the sealed vials, and will be analyzed on Jeol GCTOF. Sample solution needs to be prepared and sealed in the glove box by users. Sample solution should be prepared and dropped off at the scheduled time. Please contact facility manager or technician for scheduling and sample preparation procedure.
Electrospray Ionization (ESI) – low and high res
Samples submitted for low resolution ESI can be analyzed on Bruker HCT, or Agilent QTOF. Solid samples are preferred. If submitted in solution, the concentration should be minimum 100 µM. We prefer concentrated solution so we could dilute it to working concentration. The solvent must be specified, or solubility information must be provided. Solvents should be electrospray compatible. Some of common used solvents include methanol and acetonitrile. Solvents that should be avoided include DMSO, DMF and THF. Methanol would be the default solvent if no solvent information is specified. All salts should be avoided. Salts and buffers are in general detrimental to MS analysis and may cause ionization suppression, especially for ESI-MS. Be sure to indicate if the compound is sensitive to acid or basic condition.
Samples submitted for high resolution ESI analysis will be analyzed on Agilent QTOF. Sample will first be analyzed by low resolution ESI to determine if the mass to be measured for the expected compound is found and to confirm the choice of the solvent.
Matrix-Assisted Laser Desorption/Ionization (MALDI)
Samples submitted for MALDI analysis will be analysed on Bruker autoflex MALDI-TOF instrument. Sample should be dry solid. If submitted in solution, the concentration should be 100 µM or higher. Salts and buffers are in general detrimental to MS analysis. Salts or buffer may interfere with the matrix crystallization resulting in signal suppression. Salts may also form adduct that cause peak broadening in reduced mass accuracy and signal intensity. It is recommended that the concentration of salts and buffer should be less than 10 mM. Use of non-volatile agents such as salts and should be avoided.
Solvent–free MALDI is available for insoluble synthetic polymers or supramolecular complexes. Please contact the facility manager for details.
MS/MS
Samples submitted for ESI, or APCI MS/MS analysis can be analyzed on Bruker HCT, or Agilent QTOF. The sample will first be analyzed by low resolution ESI to determine if the mass of the expected compound for MS/MS analysis is found.
Samples submitted for MALDI-MS/MS analysis will be analyzed on Thermo LTQ-Orbitrap.
Gas Chromatography-Mass Spectrometry
Samples submitted for GC-MS analysis will be analyzed on Agilent GC-MSD. Non-polar solvents should be used. If submitted in solution, concentration should be specified. User should specify the desired GC conditions. For quantitative analysis, or special GC-MS analysis, contact the facility manager. For GCMS requiring high resolution MS, contact manager or technician.
Liquid Chromatography-Mass Spectrometry
Samples submitted for LC-MS analysis can be analyzed on Agilent 1100 HPLC / Bruker HCT MS, or Agilent 1260 HPLC / 6545 QTOF MS instrument. Solid samples are preferred. If submitted in solution, polar solvent should be used and concentration should be specified. User should provide HPLC column as well as HPLC conditions such as solvent, suggested gradient, flow rate and a HPLC chromatogram under the suggested condition. For quantitative analysis, contact the facility manager for details. For LCMS analysis requiring high resolution MS, please contact manager, or technician.
Elemental Analysis
Samples submitted for CHN analysis will be analysed on Thermo Flash 2000 elemental analyzer. Elemental analysis should be one of the last analytical techniques for synthetic compound characterization. Sample of high purity should be submitted; otherwise the measured values would not be useful. Identity of the compound should be confirmed by other techniques such as mass spec before submitting to EA. Minimum amount of solid or liquid sample should be 5 mg for CHN and 10 mg for CHNS analysis. Air-sensitive samples should be scheduled ahead of time with the EA analyst.
Samples such as soils, rocks, inorganic materials, etc, are unacceptable since their decomposition will leave large amounts of residue that may interfere with subsequent determinations.
MALDI MS imaging
Please contact the facility manager for details.
Seld-serve MS -Training and Booking
Four instruments are currently available for self-services. They are only available to researchers currently working in the Chemistry department including postdoc fellows, graduate and undergraduate students.
Waters LC-MS. This system is set up as an open access MS (OAMS) for chemists to have quick mass confirmation of compounds. It is particularly useful for polar organic compounds.
Agilent GC-MS. This is used for chemists to have quick mass confirmation of non-polar compounds with sufficient volatility and thermal stability.
Bruker HCT. Bruker HCT ion trap, coupled with Agilent 1100 HPLC, is a LC-MS system. This LC-MS can be used to perform various experiments including low res full scan mass spec analysis, tandem mass spec and LC-MS.
Bruker autoflex MALDI-TOF. It is useful for people working on supramolecular complexes, synthetic polymers and biopolymers.
Contact the facility manager to schedule training.
Trained users may book instrument and booking can be located at https://www.chem.ubc.ca/department-resources
FAQ
Mass Spec Mailing List
Users of the MS-EA facilities are advised to join the MassSpec/EA Users mailing list and you may subscribe to the mailing list at https://www.chem.ubc.ca/mailing-lists
Mass Spectrometry Services
How do I choose an ionization method?
There are many factors you should consider to choose an ionization method. Structure and size of the molecule are the two most important ones. For a specific compound, multiple mass spec methods may work. For example, you can choose EI or FD for non-polar small molecules, or MALDI for non-polar compounds with MW>1000. Similarly, you can choose ESI, or FD for polar compounds. MALDI is not preferred for small molecules with MW<700 because of matrix interference.
How different analyses are scheduled?
Generally, low res MS will be run before high res (EI, APCI, ESI, FD, MALDI). Some analyses can be performed on multiple instruments. For examples, low res EI sample can be run on either Agilent GCMS or Jeol GCTOF. Similarly, low res ESI sample can be run on either Bruker HCT or Agilent QTOF. When multiple ion sources are available on the sample instrument, ion source needs to be switched for different analysis. Please note that FD is normally on Jeol GCTOF unless EI is needed. Similarly, ESI is normally on Agilent QTOF unless APCI is needed. The waiting time for different MS analysis varies. Contact manager or technician if you have question about the MS analysis you are waiting for.
How do I submit an air-sensitive sample for mass spec analysis?
Air-sensitive samples will be analyzed on Jeol GCTOF using LIFDI probe. You need to prepare the sample solution in your glovebox and bring it to the mass spec lab. Contact the facility manager for details.
Elemental Analysis Services
How much sample do I need to submit?
About 5 mg sample should be submitted for CHN and 10 mg for CHNS analysis. Normally, 1-2 mg is needed for one CHN run and 3-4 mg for CHNS. Extra sample is required for rerun when needed.
How do I submit air-sensitive samples for EA analysis?
Please contact the EA technician to schedule the analysis. You can bring your sample on the same day when analysis is scheduled.
How do we ensure the accuracy of EA data?
Elemental composition of unknows sample is determined by using calibration factor, which is determined by analyzing a suitable certified organic standard (OAS) of known elemental composition. The accuracy of measurement depends mainly on the calibration. Certified standards are run every two or so samples in order to ensure the calibration has not drifted. They are served as QA/QC standards.
Why CHN and CHNS need to be performed at different time?
Different instrument configurations are needed for CHN and CHNS analysis. The waiting time for each EA analysis varies. Contact manager or technician if you have question about the EA analysis you are waiting for.
Why is our EA only for organic compounds?
Our EA is so-called organic elemental analysis (OEA). The analysis is based on complete decomposition and conversion of organic elements. Materials that can’t be decomposed at the temperature setting of the combustion tube (or reactor) will build up as ash on the top of reactor. This will result in the compromised data quality and also increase the maintenance work.
Self-Serve MS Services
What are available for self-service MS?
Users may be trained to run LC-MS (including ESI-MS), GC-MS (including EI-MS) and MALDI-MS.
How do I get a training and access?
Training is scheduled as needed. Contact the facility manager.
Which training should I attend?
If your compounds are polar organic, you should consider Waters LC-MS and Bruker HCT. OAMS is the easiest one to use. But, HCT offers additional advantages including MS/MS. For non-polar organic compounds, you should consider Agilent GC-MS. You should consider Bruker autoflex MALDI-TOF if you work on supramolecular complexes, synthetic polymers and biopolymers.
High Resolution Mass Spectrometry
What is high resolution mass spectrometry service?
The power of accurate mass is in the determination of the elemental composition (EC) of a compound. So-called high resolution mass spectrometry service is traditionally referred to as accurate mass measurement on the masses of interest. Accurate mass measurements are used to determine the elemental composition of molecular or fragment ions. These measurements are performed normally on high resolution mass spectrometer so that the masses are measured for a single species and not measured for unresolved or partially resolved peaks. The masses of interest are measured with enough accuracy to limit the possible elemental composition or confirm unique composition.
Why low res MS needs to be performed before submit for high res?
Generally, low res MS should be run first and the mass to be measured must be confirmed in low res full scan before submitting for high res MS.
What are requirements for high resolution mass spec samples?
Purified compound is preferred as this will avoid /minimize possible ionization suppression and ensure the ion intensity of the analyte. The mass for the ions formed from the compound in the low res full scan must be confirmed – use monoisotopic mass, not molecular weight. Correct isotope pattern for the compound should be detected. The possible elemental composition for the compound is proposed.
What are the reasons that samples might be returned?
Samples will be returned if it is impossible to measure the mass of interest. This could be 1). The mass assigned for the peak to be measured is wrong for the formula proposed, or no mass has been specified to be measured; 2). The intensity of the peak chosen for the measurement is too weak to be measured; 3). Sample provided is not enough; 4). Wrong isotope pattern is detected. This would suggest that a different compound is detected or there are overlaps due to different compounds. 5). Low res mass spectrum is not provided.
What are the reasons that no elemental composition (EC) report can be provided?
There is random error associated with the mass measured. Elemental composition (EC) report depends on accuracy of the measured mass and constraints on the compositions such as type of elements. The mass accuracy is limited by the instrument and method used for the measurement. Setting an acceptable error limit for exact mass measurement data, even 1ppm, does not assure that a measured mass corresponds to only one plausible empirical formula. A problem for high resolution mass spec sample submission is lack of elemental composition. Total number of possible elemental compositions increases exponentially with increasing mass and can be very large even for modest masses. It would be impossible to generate a meaningful report without constraints on elemental composition information. The EC report for mass >1,000 is practically not useful since it could include huge lists of empirical formulae depending on the constraints. Our task should be focus on assignment (and/or elimination) of empirical formulae, not “exact mass measurement” as stated in the ASMS guideline for exact mass measurement and elemental compositions.