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Stanford University Mass Spectrometry Vincent Coates Foundation
Vincent Coates Foundation

Sample Preparation

Before submitting your samples, please ensure they have been prepared according to the following recommended guidelines and specifications. If you have any questions, please send an email to: jpgalind@stanford.edu or  gmcken1@stanford.edu

Proteins in polyacrylamide gel

  • Samples for protein identification by proteolytic digestion and LC-MS/MS are commonly submitted as Coomassie-stained bands or spots in polyacrylamide gels.
  • The gels should be handled as little as possible to minimize contamination by dust and keratin.
  • Destain Coomassie-stained gels by soaking for at least 2 hours in 10% acetic acid, 50% methanol, and 40% H2O with at least two changes of this solvent. If the gel still has a Coomassie Blue background, then continue destaining until the background is nearly clear.
  • Sypro Ruby and other fluorescent stained gels should not require an additional destaining step.
  • After destaining, soak in pure water until pH is neutral.
  • The spot or band of interest should be excised cleanly, excluding all of the surrounding blank gel; the goal is to maximize the ratio of protein to gel.
  • The maximum size of a gel band should be 1.5 cm. Cut the excised gel into small pieces (1-2 mm square) and place in a clean Eppendorf vial with a 1% acetic acid solution.
  • Wet samples should be shipped on dry ice. Dry gel pieces may be shipped at room temperature.
  • In-Gel Protocol

Proteins in solution

  • Solution samples for identification will be reduced and alkylated, followed by protein digestion.
  • Samples should be shipped on dry ice.
  • Non-acceptable buffers include NP40, CHAPS, Triton X, and PEG. 
  • Contact the proteomics team if SDS needs to be used.

Tissue samples

  • Weigh your dry tissue samples before submitting them.
  • If possible, don't bring more than 50 mg. Our instruments are highly sensitive and don't require large sample inputs. 
  • Fresh frozen is preferable; if handling FFPE, please contact the SUMS proteomics team. 

Magnetic Beads

  • After following the Magnetic Beads kit, do multiple PBS washes (5-10) before submitting the samples. 
  • Don't freeze the beads
  • Contact SUMS to arrange a drop-off time, as they have to be processed the same day.
  • Same-day magnetic beads drop-off is strictly forbidden.