Mass Spectrometry Facility



Accurate Mass Determination

How to get an accurate mass measurement for your samples.     

Accurate Mass (AM) determination is sometimes also called High Res. The name represents the family type of instruments, which mainly but not always, being used for this procedure.   

Samples are run by automation to meet samples demand and limited instrument time to increase efficiency and keep price low while going paperless to save some trees!

We run samples on demand, usually once a month or as needed. 

If you are about to publish and need to get Accurate Mass (AM) determination for your samples, otherwise known as High Res,  please call (250-721-7183) or e-mail   and 

Reminder: Please check for the latest version before every submission.
  1. Create and FOM account for charges. 
  2. The cost per sample is $50 and will be charged if the desired mass is found or not. So make sure to prepare your sample properly and it’s a good idea to check your sample on the walkup MSQ instrument.
Sample info
  1. Create a .doc or .pdf file using ChemDraw which includes the following information:
  2. Sample name:
    (PI-initial-sample e.g. FH-AW-11-345A, JW-MB-33-D, DB-ENA-11-6 ,
    please make it short and no “ ; , . and other characters $%&* etc. ) 
  3. Structure
  4. Empirical formula (C33H54Br3SO2)
  5. Exact mass with 5 decimal points. (one of the options on Chemdraw or use this tool
  6. Name the file: PI-Initials-date of analysis
Uploading the information:
  1. Log in to CMSF Connect site – use your NetLink ID.
  2. Search for the Orbitrap folder on the left side and click. (You can find a copy of this SOP there)
  3. Find the current year folder (Apr 202x-Mar 201x)
  4. Find the next date for the sample run (202x-mm-dd)
    1. If there is no future date set, please e-mail me to set one. Please include your name, supervisor name, number of samples and by when do you need those done. 
  5. Add your .doc/.pdf file to the folder – you can replace and modify this file at a future time.
  6. Find the .xlsx workbook and “check out” by pressing the small dropdown box at the end of the yellow box showing when you hover over the filename.
  7. Add your samples to the .xlsx file by filling the name, empirical formula and monoisotopic mass to the table.
  8. We are now running always in both ionization mode +ESI and –ESI 
  9. Save the file back to its location. 
  10. “Check-in” by pressing the small dropdown box at the end of the yellow box showing when you hover over the filename.
Sample preparation
  1. Prepare a stock solution 
  2. 1mg/ml (1000ppm) in MeOH, ACN, H2O, IPA or any ratio mix of those. 
  3. Make sure your sample fully dissolved  
  4. If your samples do not dissolve use 100ul of another organic solvent, DCM, toluene and add one of the other common solvents. IPA usually works best. 
  5.  Mark the sample clearly with the same name on the datasheet and Xls file. 
  6.  Dilute you sample 1:10 (100ppm, 100uL in 1ml) and 1:100 (10ppm, 10uL in 1 ml) with same solvents in auto-sampler vials.
  7. Mark the auto-sampler vials clearly indicate sample name and #. NO stickers 
Sample submission
  1. Bring the sample to ELL066 on the day of the run no later than 11:00. 
  2. Trays are colour-coded. Chose the one showing the same colour as the excel table.  
  3. Put your sample in the dedicated tray each sample in the right number spot.
  4. Positions: A- most dilute 10ppm, B –mid dilution 100ppm, C- concentrated 1mg/ml
  5. If your sample requires cooling put the tray in the freezer and let me know.

Good luck getting your desired results – results will be showing up in the same shared folder and you will be emailed as soon as results are available

We welcome any feedback you might have on this SOP

Self Service / Open Access Lab

Most of the instruments in the department detailed below are available for self-use after proper training. 

If you know which instrument you would like to use just create an account on FOM or use your existing account.

If you don't know which instrument would work best for your research project to set a time for consultation 

To create a new account:

  • You will need a FAST account number from your supervisor 
  • Don't use your UVic NetLink ID password. you may use your NetLink ID user if you like

After heaving a working account:

  • Make sure you have a current WHMIS (within the last 3 years) 
  • Send a copy of your WHMIS certificate by  
  • Apply to be trained on your instrument of chose choosing the instrument from the list on the right-hand side of the FOM 
  • Provide your availability in the next two week
  • Training could be scheduled within two weeks
  • Follow up with an e-mail if there was no reply after a week

Probe-MS Analysis


The Finnigan TRACE DSQ EI-MS is equipped with a Direct Sample Probe system (Thermo) allowing for quick sample introduction directly to the mass spectrometer ion source where the sample is vaporized and subsequently ionized by electron impact.

This system is best suited for the analysis of solid or liquid samples that are difficult to elute using gas chromatography, for example, samples containing thermally labile or highly polar compounds. 

This analysis is not offered for self-use due to the process the probe must be inserted into the ion source to avoid costly instrument failure.   

Instructions for submitting samples for direct insertion probe – mass spectrometry (DIP-MS):  

1).  If you are interested in DIP-MS analysis of your samples please contact either  and  and provide the following information:

  • How many samples to be analyzed. 
  • For each sample note what the expected molecular formula is and send a file showing structures.  If this information is not known it is ok but makes note of this and any info that might be helpful (ie. Starting materials).
  • Note if the sample is pure or a mixture if it is stable or any other info that may be relevant for accurate analysis.  Air and moisture sensitive samples can be analyzed!
  • How soon you need the analysis.  

2).  After contacting the MS facilities we will email you back to arrange for you to pick up the sample cups that are inserted into the probe and also time and day we plan to run the analysis.

3).  When handling the DIP sample cups (figure 1) make sure to use clean tweezers and wear clean gloves to avoid contaminating the cup with other chemicals or oils from your skin.

4).  You can load either liquid or solid samples into the DIP cups.  Solid samples can be placed directly into the sample cup using a spatula or dissolved first and injected into the cup.  Liquid samples should be injected into the sample cup.  Very little material is needed for successful analysis so if it is clearly visible in the cup it should be enough.  Please do not overload the sample cups and avoid getting material on the outsides of the cups as this can contaminate the probe.  See Figure 2 for examples of loaded cups.

5).  After loading the sample cup it should be placed in a small vial and labelled.  The 2 mL Agilent vials used with the GC-MS or UPLC systems can be used for this (see figure 3).  If your sample is a solid powder and falls out of the sample cups easily using an insert like a small piece of kimiwipe can be helpful to keep the cups upright.  We also have small vials with an inner conical bottom which works well to keep the loaded DIP cups upright.

6).  Drop off the loaded sample cups in Elliot 066 at the arranged time of analysis.  Note that unless you are confident the sample is stable it is best practice to prepare the sample right before you drop them off.

7).  We will email you with results after the analysis.


Air Sensitive Probe-MS Analysis

Air or moisture-sensitive probe MS analysis

Overview:  The direct insertion probe system in the UVIC mass spectrometry facilities is equipped with a small glove box that can be purged with dry N2

This allows for easy and convenient analysis of air and/or moisture-sensitive complexes. 

Examples of some air-sensitive organometallic complexes successfully characterized can be found in the following reference. (J. Penafiel, A.V. Hesketh, O. Granot, J.S. McIndoe, Dalt. Trans. 2016, 45, 15552-15556)


Please review the instructions given for Probe-MS Analysis above.

Follow those instructions however load the sample into the DIP sample cups in a glovebox. 

If your samples are very air-sensitive once the loaded sample cup is placed in a small vial it is a good idea to place this into a second larger vial to further prevent any air exposure once the vials are removed from the glovebox.


Polaris-Q DSQ (GC-MS)

Gas Chromatography system with MS

Brand: Thermo

GC Model: Polaris-Q

MS Model: DSQ

Ionization: EI or CI (Methane)

Mass range: 0-1000 amu

Resolution: unit 

Sample introduction: syringe injection, Direct Probe (incl air sensitive) 

3800-2200 (GC-MS)

Gas Chromatography system with MS and two other detectors

Brand: Varian (currently supported by Bruker)

GC Model: CP-3800

Sample introduction: syringe injection, SPME

Injectres: split/splitless and PTV


ECD- Electron Capture Detector - selectivity to Cl and other halogen containing compunds.

FID - Flame Ionization Detector - general use for all hydrocarbon compunds heaving a C-H bond.

MS Model: Saturn 2200

Ionization: EI or CI (Methanol)

Mass range: 50-1000 amu

Resolution: unit


Ultimate 3000 - Orbitrap (LC-MS)

Mass Spec 

Brand: Thermo  

Model: Exactive (not plus nor Q and not even HSD)

Ionization:  ESI 

Mass range: 50-4000 amu (m/z)

Resolution: 140,000

Mass Accuracy <1ppm

Software: Excalibur 

Liquid Chromatography system 

Brand: Thermo  


Max flow: 10ml/min

Max pressure: 600 BAR / 9000 PSI

Max injection 20uL

Max injection 20ul and up to 200ul with alternative injection loop 

Column: recommended 2.1/3/.4.6 mm ID with 5-2.6 particle size Detector 1: DAD 190-900nm

Software: Chromeleon 7.3

Ultimate 3000 - DAD - MSQ (LC-DAD-MS)

This is a complex system constructed of two LC system sharing the DAD and MS as detectors. One of the system is set as analytical system while the other as Semi-prep system.

Liquid Chromatography system (I)

about the instrument 

Application: Semi-prep in Reverse Phase or HILIC mode 

Brand: Thermo  

Model: HPG-3000

Max flow: 10ml/min

Max pressure: 600 BAR / 9000 PSI

Max injection 2.5ml

Column: recommended 10mm ID 

Software: Chromeleon 7.3

Liquid Chromatography system (II)

about the instrument 

Application: Analytical in Reverse Phase or HILIC mode 

Brand: Thermo  

Model: HPG-3000

Max flow: 10ml/min

Max pressure: 500 BAR / 7500 PSI

Max injection 20ul

Column: recommended <4.6 mm ID (2.1/3/.4.6 mm ID with 5-2.6 particle size)

Software: Chromeleon 7.2.6

Mass Spec

Brand: Thermo  

Model: MCQ Plus

Type: single qoude

Ionization:  ESI 

Mass range: 50-2000 amu (m/z)

Resolution: 2,000

Mass Accuracy: 0.1 Da

Software: mix

Waters (UPLC- DAD - MS)

Ultra high-pressure Liquid Chromatography system

Application: Analytical in Reverse Phase or HILIC mode 

Brand: Waters

Model: Acquity UPLC H-Class (quaternary)

Max flow: 4ml/min

Max pressure: 1050 BAR / 15,000 PSI

Max injection 250ul 

Column: recommended <=2.1 mm ID with <2.6 particle size (1.7 or 1.3)

Detector 1: DAD 190-800nm

Detector 2: QDa - mass range 50-1250, 30ms polarity switching

Software: MassLynx 4.3

Agilent 1100 (HPLC - DAD - FLD)

Liquid Chromatography system

Brand: Agilent 

Model: 1100 

Max flow: 5ml/min

Max pressure: 400 BAR / 6000 PSI

Detector 1: DAD both UV and Vis Range: 190-900nm 

Detector 2: FLD

Software: ChemStation ChemStation B.04.03

Agilent 1200 ( HPLC - DAD)

Liquid Chromatography system

Brand: Agilent 

Model: 1200 

Max flow: 5ml/min

Max pressure: 400 BAR / 6000 PSI

Detector 1: DAD 190-900nm

Software: ChemStation B.04.03

LCQ Classic (Ez-MS direct infusion )

Mass Spec with Direct Infusion (Easy-MS)

Brand: Thermo  

Model: LCQ Classic 

Type: 3D Ion trap

Ionization:  ESI 

Mass range: 50-2000 amu (m/z)

Resolution: 2,000

Mass Accuracy: 0.1 Da

Software: Excalibur

The system that we are using to request training on an instrument, book an instrument and get access to an instrument (after training) is available here

FOM manual is available here

If you have any issues please

  • Office (Elliott 066c):                     250-721-7183 - voice mail
  • Analytical lab (Elliott 066,066b):   250-472-5028
  • Easy-MS Lab (BWC B214):           250-853-3642
  • Departmental Fax:                       250-721-7147 

Mailing address

Department of Chemistry
PO Box 1700  Stn CSC
Victoria, BC V82 2Y2


Courier address

Department of Chemistry
University of Victoria
Elliott Building Room 301
3800 Finnerty Road
Victoria, BC V8P 5C2

Facility Manager: , B.Sc., Ph.D., MBA

Assistant Manager , B.Sc., M.Sc., Ph.D.