Biomolecular Mass Spectrometry

Molecular Mass Measurements

<h2 class="heading-underline">Molecular Mass Measurement</h2>

<table class="heading-underline" cellpadding="0" cellspacing="0" style="width:500px;border: 0px solid white;margin-left:auto;margin-right:auto;"><tbody><tr><td style="border: 0px solid white"><img alt="Molecular mass measurement" src="/biologicalsciences/images/molecularmass_1.png" /></td><td style="text-align: left;vertical-align:text-top;border: 0px solid white"><strong>Useful for:</strong><ul><li>Confirming correct synthesis/expression</li><li>Establishing purity</li><li>Detecting PTMs</li><li>Checking chemical derivitisation</li></ul></td></tr></tbody></table>

Using LC-MS, protein samples are desalted immediately prior to mass measurement.

With this approach, in most cases, buffer exchange prior to analysis is no longer required (N.B. any PEG or glycerol must still be removed before analysis).

Ideal sample volume is 20 uL at 20 uM concentration.

Details of method used to measure concentration should be provided. Internal users have the option of using the VersaWave spectrophotometer in the MS Facility to determine concentration.

Some sensitive proteins are not amenable to LC-MS degrading during analysis.

In these cases we can buffer exchange samples into a volatile ammonium buffer by dialysis or using a buffer exchange spin column. This will be carried out by the Facility immediately prior to analysis.

Oligonucleotide mass measurement

Oligos require purification before analysis to remove metal ions, particularly sodium. The most successful methods of purification are dialysis against 200 mM ammonium acetate or using precipitation methods.

Minimum sample volume is 20 uL at 50-100 uM concentration.

Accurate mass measurement

Molecules below 2000 Da in mass can be determined to within 5 ppm.

Small organic molecules and peptides can be submitted in lyophilised form or in solution using an acceptable solvent system.

Acceptable solvent systems can be formulated from: water, acetonitrile, methanol, propan-2-ol, hexafluoropropan-2-ol and chloroform.

Solvents to be avoided are the less volatile ones such as dimethylformamide, and less stable ones such as tetrahydrofuran. DMSO is acceptable only if present at below 1% v/v.

Sample analysis

Internal users can arrange to analyse their samples at any time. For new users, please come to the MS lab and have a chat with a member of the Facility staff and we can give you all the information that you need to get started. We now require that University of Leeds users perform their own data processing and analysis and we will provide the required trainng and as much help as you need to do this. 

Sample analysis can be requested through our online booking system iLab. Internal users can log in with their Univeristy credentials. 

Please note that by submitting samples to the MS Facility for analysis you agree to our conditions of service and publications policy. A copy of which can be found here.

Users external to the University can find additional information here


The concentrations and volumes stated above are provided as a guide only.

We will still accept and attempt MS analysis on samples of lower (or unknown) concentration and/or volume.

Where analytes are only stable outside of their preferred buffer for short periods of time, buffer exchange can be performed in the mass spec lab immediately prior to analysis. Please contact us in advance to arrange this if required.