MALDI-TOF Sample Requirements

Sample Submission Forms

Peptide Mass Fingerprint Submission Form
Protein Molecular Weight Submission Form

Protein Samples

Protein samples for molecular weight determination may be submitted as a solution or as a lyophilised powder. Samples containing a single protein are preferred, however, in a limited number of cases, simple mixtures can be differentiated during spectroscopy.

Although the MALDI can tolerate the presence of low amounts of salt and non-ionic detergent, these should be avoided if possible as they will suppress the signal. Ionic detergents should never be used.

In the submission form, be sure to advise us of the solvent in which the sample is dissolved, or was dissolved prior to lyophilisation.

If there are special handling considerations for your sample be sure to discuss them with us prior to sending the sample and to note them on the submission form.

Digest Samples

Digest samples should be digested by you. The sample may be submitted as a solution, lyophilised powder or in the gel with the peptides still to be extracted, in which case we will sonicate with a minimal volume of 20% Acetonitrile/0.1% TFA.

When preparing samples certain precautions must be taken to ensure good results are obtained. Only AR grade reagents (preferably HPLC grade) should be used. Iodine free iodoacetamide (iodoacetamide which contains iodine will be slightly yellow) should be used when alkylating proteins. Extreme care should be taken to avoid keratin contamination, as a speck of dust can easily overwhelm a mass spectrum making identification of the desired protein impossible. Precautions that should be taken include working in a hood, filtering gels, wearing powder free gloves, a hair net and a clean lab coat.

The quantity of protein should also be considered prior to preparing samples. If MS/MS analysis of a sample is required then a greater amount of protein is required than if only a Peptide Mass Fingerprint is required, and de novo sequencing requires more again. Be careful using some of the more sensitive stains, which are still compatible with mass spectroscopy, as the quantity of protein detected by these stains is generally too low to yield a good mass spectrum, especially if MS/MS is required.

Even though MALDI can handle the presence of some salt, salt contamination in the sample will suppress the signal. This effect is generally accommodated by increasing the laser power, however this will lead to poorer resolution and lower the signal-to-noise ratio. Low amounts of detergents can be tolerated, but should be avoided, and ionic detergents such as SDS should never be included in the sample buffer.

A strategy to overcome low protein concentration and high levels of salts is to use ZipTips. These desalt the sample and concentrate the peptides in a smaller volume. If you wish to use this procedure before sending us the sample, be aware that it can lead to the loss of certain peptide peaks, and the spectrum may still have a weak peptide signal. The best strategy to achieve good results is to ensure the sample is submitted in a good condition, with no contamination, a low salt content and an adequate amount of protein, and to liase with us prior to submitting your sample.