Department of Chemistry   University of Oxford


Small molecule open-access mass spectrometer system - ground floor, lab 20.062

The small molecule open access system on the ground floor is intended for walk up use. After an initial introduction session you are free to use the system, however it is important you follow the instructions set out below regarding samples preparation, login of samples and obtaining your mass spectra.










Sample preparation

A basic rule for small sample preparation (<1500amu) is to aim for between ~100 micrograms of analyte per millilitre of solvent. Where samples are an unknown concentration they should not be run on the system.

1. Dissolve the sample in any organic solvent (eg DCM, CHCL3, EtOAc, MeCN, MeOH) or H2O to a concentration of 1mg/mL.

2. Take 100uL of this solution and dilute it with 1mL of either methanol, acetonitrile or water (or any combination of these solvents).

3. If there is any precipitate in the resulting solition it must be filtered before running the sample otherwise this could cause the injector to fail.

3. Placed the solution in a 2mL sample vial with a screw or snap cap lid (available from stores).

4. Do not use Trifluoroacetic acid (TFA) in your samples. If you need to acidify your samples use formic acid.

5. Do not use Tetrabutyl ammonium (TBA) in your samples this will contaminated all subsequent samples run on the system.


Guidelines for sample login

1. Make sure you pay close attention to the autosampler labelling and where to place your sample. The wrong position will stop the system in the middle of the queue and will need technical assisence to re-start.

2. Take care when putting samples in the autosampler tray as the sampling arm may start moving.

3. You may login up to a maximum of 10 samples at a time. In the interests of fair usage please do not attempt to login more than this number of samples.

3. A single sample will take aproximately 2 minutes from injection to mass spectra being available.

4. Please remember to remove your vial from the autosampler tray after it has been run.

5. Results can be found in the form of a pdf on: //chem-ds5/massStore.


Open access results

Samples run on the open access system are automatically processed and a pdf is created from the spectrum. This is emailed to the user. A copy of the report style can be see below. The original masslynx data files are backed up and stored offline.

Example of OA report


Protocol and Safety in the mass spectrometry labs

No lab coats to be worn in any of the MS labs.

Open access autosampler is in continuous operation: Care should be taken not to touch it when submitting samples.

Sources are hot! (usually between 100 and 350oC). Take care when cleaning.

Never remove or tamper with any part of the mass spectrometer system. If a instrument is not working please report to a member of the MS facility staff.

Data – you are responsible for keeping it safe. For all instruments other than open access – make sure you remove it from the instrument computer hard drive within at least 1 week. You may keep it on MassStore

Please read safety information on the mass spectrometry website and all information provided at Mass Spectrometer terminals























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