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Mass Spectrometry Facility

EB-38, Department of Chemistry,
University of Alberta,
Edmonton, AB
Canada T6G 2G2

If you wish to submit a sample to the mass spectrometry laboratory for MS analysis, please follow the guidelines listed for each mass spectrometry technique.   In all cases, fill out a sample submission form and please indicate the proposed molecular formula, the proposed molecular weight, and include a diagram of the proposed structure.   Any questions you may have regarding sample preparation, data interpretation, or method of analysis are welcome, especially if the amount of sample is limited or you require special sample handling.   Please feel free to talk to any of the mass spectrometry laboratory personnel with your questions or concerns, we are here to help and are happy to do so.

Users that are from the University of Alberta but not from the Department of Chemistry require an Indent form, that must be completed by their home department.   Users that are not from the University of Alberta campus require a purchase order (P.O.).   Please see our price list for details regarding pricing, volume discounts are given.

The sample storage facilities available in the mass spectrometry laboratory include a refrigerator (4C), and freezers at 15C, 25C, and 80C.

Any special safety or sample handling precautions the operator should take with your sample should be indicated on the sample submission form.   Please note that the Mass Spectrometry Laboratory is NOT equipped to handle radioactive samples.

  1. Electron Impact Ionisation(EI)
    1. Low Resolution
    2. High Resolution
    3. Gas Chromatography (GC)
  2. Chemical Ionisation (CI)
    1. Low Resolution
    2. Gas Chromatography (GC)
  3. Electrospray Ionisation (ESI)
    1. Low Resolution ESI
    2. High Resolution (Exact Mass) ESI
    3. Liquid Chromatography - ESI (LCMS)
    4. ESI MS/MS and/or LC MS/MS
  4. Atmospheric Pressure Photo-Ionisation (APPI)
    1. Low Resolution APPI
    2. High Resolution (Exact Mass) APPI
    3. Liquid Chromatography - APPI (LCMS)
  5. Matrix-Assisted Laser Desorption / Ionisation (MALDI)
    1. MALDI MS
    2. High-Resolution (Exact Mass) MALDI MS
    3. MALDI MS/MS
  6. Protein Identification
    1. In-solution digestion MALDI MS and/or MALDI MS/MS and/or LC MS/MS 
    2. In-gel digestion MALDI MS and/or MALDI MS/MS and/or LC MS/MS

Electron Impact Ionisation(EI)

Samples submitted for EI analysis will be analysed on one of the Kratos MS-50 instruments.   The samples (minimum 50 nanomoles or 25 g for a compound of 500 u) should be submitted as solids or neat liquids, preferably in a or 1 dram vial.   This applies to low or high resolution analysis or for gas chromatography analysis.

For gas chromatography (GCMS) analysis users should specify the desired GC conditions to use, i.e., injection temperature, oven programme, carrier gas, and type of column as well as provide a chromatogram obtained under the same conditions.   The solvent used to dissolve the sample should be indicated.

Chemical Ionisation (CI)

The same sample submission procedures apply to samples for CI as to samples for EI.   Users are asked to suggest a reagent gas for CI from a choice of ammonia (NH4), isobutane ((CH3)2CHCH3), and methane (CH4).   Other reagent gases are also possible by special request.

Electrospray Ionisation (ESI)

If you require both low and high resolution ESI analysis then please follow the sample submission procedure for high resolution ESI.

Low Resolution ESI

Samples submitted for low resolution ESI analysis will usually be analysed on the  Agilent 6220 oaTOF.  Indicate on the sample submission form which electrospray compatible solvent(s) is (are) most appropriate for your sample.

High Resolution (Exact Mass) ESI

Samples submitted for high resolution ESI analysis as well as samples requiring special sample handling will be analysed on the Agilent 6220 oaTOF mass spectrometer.   The sample (minimum 1 nanomole or 0.5 g for a compound of 500 u, free from involatile buffers and surfactants) will first be analysed by low resolution ESI to determine if the expected compound is found and to confirm the choice of solvent.   The sample should be submitted as a neat liquid or dry solid to ensure that sample decomposition does not occur.   On the sample submission form, please indicate which electrospray compatible solvent(s) is (are) most appropriate for your compound.

Liquid Chromatography - ESI (LCMS)

Samples submitted for LCMS will usually be analysed on the HP 1100 MSD mass spectrometer, or the Agilent 6220 oaTOF.   It will normally be required that the user provides the HPLC column necessary for completing the analysis (check with the us to see if a column is available for your sample).   The user should normally provide suggested HPLC conditions, e.g., solvents used, suggested gradient and HPLC flow rates as well as an HPLC chromatogram collected under the suggested conditions.   However, if this information is unknown then assistance in the development of the necessary HPLC conditions will be gladly provided (see our price list ).   HPLC conditions should not include buffers and trifluoroacetic acid (TFA) should be avoided, as these compounds are not compatible with electrospray analysis.

Please submit samples (minimum 1 nanomole or 1 g for a compound of 1000 u) in 12 x 35 mm ( dram) screw-capped vials (preferably with TFE, i.e., teflon caps, available from the storeroom).   It is preferable that the sample be submitted as a dry solid or neat liquid.   On the sample submission form, please indicate suggested solvent(s) for your compound.   If the sample is in solution, then the concentration of organic solvent must be less than or equal to the organic solvent concentration used at the start of the HPLC gradient (for reversed phase HPLC).   If you have any questions or concerns, especially regarding sample handling, please contact any of the laboratory personnel or e-mail Dr. Randy Whittal at the address listed below.

Atmospheric Pressure Photo-ionisation (APPI)

Samples submitted for low or high resolution APPI or APPI LCMS analysis will be analysed on the Agilent 6220 oaTOF mass spectrometer   The sample (minimum 10 nanomole or 5.0 g for a compound of 500 u, will first be analysed by low resolution APPI to determine if the expected compound is found.   The sample should be submitted as a neat liquid or dry solid to ensure that sample decomposition does not occur.

ESI MS/MS and/or LC MS/MS

Samples submitted for ESI MS/MS or LC MS/MS analysis will be analysed on the Waters Q-TOF Premier mass spectrometer or the AB Sciex QTRAP 2000 mass spectrometer.   The sample will first be analysed by low resolution ESI to determine if the expected compound(s) is (are) found and to confirm the choice of solvent(s).   The sample (minimum 1 nanomole or 1 g for a compound of 1000 u) should be submitted as the neat liquid or dry solid that is free from surfactants and involatile buffers.   Users should discuss experimental details with the instrument operator.  The AB Sciex QTRAP 2000 is capable of quantitative analysis via LC MS/MS using the MRM (multiple reaction monitoring) scan mode.

Matrix-Assisted Laser Desorption / Ionisation (MALDI)

MALDI MS

Samples submitted for MALDI analysis will be analysed on the AB Sciex Voyager Elite MALDI TOF.   The sample (minimum 0.1 nanomoles or 0.1 g for a compound of 1000 u) should be submitted preferably as the dry solid or in a solution free from surfactants (most buffers are OK).

High-Resolution (Exact Mass) MALDI MS

Samples submitted for high-resolution (exact mass) MALDI analysis will be analysed on the Bruker Daltonics Apex-Qe FTICR MS.   The sample (minimum 0.1 nanomoles or 0.1 g for a compound of 1000 u) should be submitted preferably as the dry solid or in a solution free from surfactants (most buffers are OK).

MALDI MS/MS

Samples submitted for MALDI MS/MS analysis will be analysed on the Bruker Daltonics UltraFlextreme MALDI TOF/TOF MS mass spectrometer.   The sample will first be analysed by low resolution MALDI to determine if the expected compound(s) is (are) found.   The sample (minimum 0.1 nanomoles or 0.1 g for a compound of 1000 u) should be submitted as the dry solid or in a solution free from surfactants (most buffers are OK).   Users should discuss experimental details with the instrument operator.

Protein Identification

Samples submitted for protein identification will typically be analysed by LC MS/MS analysis on the Waters Q-TOF Premier mass spectrometer after the protein has been digested via enzymatic digestion (usually trypsin). The person submitting the sample will be responsible for carrying out the in-gel digestion. Please contact us for the current protocol.   Supporting evidence may be obtained through MALDI MS or MALDI MS/MS analysis.  We recommend that you digest at least 50 to 250 ng of protein per spot for successful identification; however, as little as 10 ng of protein per spot may be sufficient (dependent on many factors).  We recommend that you review our guide for successful protein identification.



For further information, please contact:

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