Proteomics Area
Mass spectrometry is a technique very sensitive to the presence of contaminants, which if in excess could totally invalidate the analysis. Therefore it is essential to minimize sample contamination.
Keratins are ubiquitous proteins from the skin, hair, dust, clothes, chemicals, etc. The total elimination is practically impossible, but to avoid the signal suppression of the proteins of interest it is necessary to use particular precautions in the sample preparation and manipulation. A particularly careful working environment is the best prevention and that's why we prefer to run/cut the gels in our laboratory. Furthermore, it is strongly recommended to wear nitrile gloves without dust at all times of sample preparation. Latex gloves often contain starch, and therefore many proteins. It is preferable to use single-use or dedicated containers (eg centrifuge tubes).
If you decide to prepare gels, it is essential to avoid touching containers and gels with bare hands; use clean containers dedicated to the staining (and not, for example, those used for Western blot) and close with a lid during staining/storage. If there is no cover, use silver paper and never use Parafilm. Do not lean on the gel, scratch your head or beard during the interpretation of the bands. If you take the gel from the container (eg. for scanning, cutting), thoroughly clean the scanner with water (no soap!). Always use new solutions to prepare and run gels, including running buffers and sample buffers. It is preferable to use TCEP as a reducing agent rather than b-mercaptoethanol or DTT.
Other observed proteins are often BSA, immunoglobulins and other serum proteins. These usually come from cell culture media and can be reduced by repeated washing of cell pellets.
In the case of plasma/serum analysis it is necessary to use specific protocols for the elimination of the most abundant proteins.
Polymers are the most harmful contaminants, since in addition to suppressing the signal they tend to stick to HPLC columns or capillaries, damaging the system or at least causing a serious memory effect on subsequent LC-MS strokes. Most polymers ionize peptides more easily and this means that even small amounts can be detrimental to the experiment. The polymers most frequently observed are various forms of PEG, present in some plastics; but also in soaps, hand creams (wearing gloves is essential!) and detergents. It is not always easy to trace the source of a contamination from polymers, but a certain source is the Parafilm, to avoid absolutely to close tubes or bottles of solvents, or gel trays etc. Furthermore, detergents should not be present in the samples to be subjected to MS, for this reason the analysis is always preceded by PAGE or chromatography.