General Guidelines for Handling Protein Gels

A primary goal of working with gels intended for downstream LC-MS/MS analysis is to avoid contamination with foreign proteins. These proteins are typically human keratins derived from human skin or animal keratins from the clothes we wear. These proteins can be transferred to the gel or items which contact the gel (plates, buffers, stains, tools, etc.) via direct contact or by being exposed to the air, as dust in the air is composed of human skin cells. While gels are not dangerous to work with, it is beneficial to approach working with them as you would if you were working with materials which had to be kept sterile or were radioactive, that is, approach them with a mind-set aimed at minimizing contact and contamination.

Running Gels

  • We recommend the use of pre-cast gels from any of the major vendors. This is the first step to minimizing gel contamination with foreign proteins.
  • Use the same care in preparing the electrophoresis apparatus and gel buffers as you would in excising spots or bands from the gel.
  • Use nitrile gloves, do not use latex gloves
  • Wash your gloves frequently with water and shake dry or dry with a lint free wipe
  • Avoid direct contact with buffer reagents
  • Prepare buffers using clean glassware
  • Do not leave buffers exposed to the open air any longer than is necessary
  • Avoid working in a hood which pulls air into the hood, use a laminar flow or “dead air” hood instead

Staining Gels

  • We recommend the use of Coomassie Brilliant Blue or MS-compatible silver staining kits from a major vendor, this avoids potential contamination from user-prepared stains
  • If preparing the stain yourself, follow the same guidelines outlined above to avoid contamination
  • Transferring the gel from the plate to the staining dish is the most common source of contamination, try to avoid direct contact with the gel or with the water in the staining dish
  • When staining, keep the dish covered to avoid exposure to air

Excising spots or bands

  • Avoid direct contact with the gel
  • Many tools are available to assist with excision: scalpels work well for bands, Harris punches work well for spots, the Gel Company sells a variety of tools, including wire grid cutters to cut many bands from a gel lane simultaneously
  • Make sure the tools you work with are clean: rinse them regularly with water and dry with a lint-free wipe
  • We have already rinsed the tubes/plates provided but it is good practice to rinse them again with water
  • After placing the spot or band in the tube or well it is not necessary to cover them if they are to be shipped immediately. If you plan to store them, cover them with 0.1% acetic acid.
  • Store gel spots or bands at 4 C