Sample Prep Guidelines and Tips

Avoiding Contaminants:

For mass spec-based proteomics, the presence of certain contaminants can be extremely detrimental.  The main offenders are keratin (from skin/hair/dust), detergents and some polymers. As keratin can be found in circulating lab air as well as on our person, it is important to take extra care to work in a clean area, wear gloves at all times, and keep all materials (including gel apparatus, buffers, tubes, etc.) covered and free of dust.  More detailed tips can be found here.

Detergents and polymers that are difficult to sufficiently remove are Triton, Tween and PEG. We typically will not accept samples that have been processed with these reagents.  Alternative reagent suggestions can be found here. If you have questions or concerns regarding any of your reagents, please contact us.

Gel Band Prep:

In-gel digestions are most successful with Coomassie stained gels. Silver stain or Sypro Ruby can also be used; however, silver stain requires use of a mass-spec compatible staining kit. Coomassie or Sypro Ruby gel spots may be submitted dry or dehydrated or in de-staining buffer (some sample loss may occur over time). Silver stained gel spots should be submitted in 1% acetic acid.

To minimize keratin contamination of your gel, follow the tips found here. Cut out bands as tightly as possible to minimize excess gel material. Chop band into ~1mm² pieces and place in a clearly labeled microcentrifuge tube.

Samples in Solution:

Protein extracts or purified proteins that are in-solution may be submitted dry or in-solution. If submitting samples dry, please indicate the estimated amount of total protein by weight. If submitting samples in solution, please indicate the components of the solvent/buffer and the total protein concentration. Our standard, in-solution digest requires 30-50µg of total protein (50µg is best).

Samples for MALDI-TOF

General sample prep guidelines can be found here.  The MALDI-TOF can be operated as full-service or self-service.  To request full-service, follow the General Submission Guidelines above.  To inquire about training for self-service, please contact us.