Sample Submission

Mass Spectrometry Sample Preparation Guidelines

Prior to sending samples, investigators are recommended to contact the facility to discuss the required analysis. This is necessary to ensure that the most efficient and cost-effective analytical methods are employed. Samples are normally analyzed in the order of their receipt, but special arrangements can be made for unstable samples. A sample submission form and guidelines should accompany each set of samples.


General guidelines for sample preparation:

 When preparing samples for mass spectrometric analysis, it is best to limit sample manipulations. When dealing with solution samples, never bring the sample to complete dryness. Salts and detergents will interfere with MS analysis of solution samples. Based on extensive studies, we have found that SDS-PAGE or 2D IEF-SDS-PAGE is the best method for recovery of low quantities of protein

  1. The sample should be dissolved in pure water or shipped completely dry if possible. Try to avoid sending samples in high ionic strength buffers as this may interfere with the ionization process. Organic buffers, such as tris and guanidine, and inorganic buffers, such as PBS, are well known for suppressing the ionization process and should be avoided if possible.
  2. If the sample is shipped in solution containing any salt, please provide an estimate of the salt concentration possible. Also, providing a list of the salts and buffers that might be present in the solution is also extremely helpful.
  3. Any amount of sample can be submitted for analysis. Due to the fact the ionization process and detector sensitivity are sample dependent, it is rather difficult to specify a minimum amount of sample necessary for analysis. The general rule of thumb is, “The more the better”.
  4. A list of information about the sample is usually necessary. This usually includes such information as sample type (peptide, protein, etc.), expected molecular weight, purity, etc.
  5. Radiolabeled samples may not be submitted for mass analysis.
Tips:Protein/peptide solutions in 10 μM volatile buffers can sometimes be analyzed directly while samples with higher salt concentrations require prior C18 or C4 ZipTip desalting.

Sample amount recommendation:
  •   Deliver more accurate data for larger proteins – MW above 50 kDa.
  •   Sample amount = 500 attomols of peptide is routinely identified.
  •   Recommended amount is 1-10 fmol.
  •   Coomassie blue and digestion compatible silver stained protein bands are appropriate.
MALDI-MS & – Tof/Tof
  •   Suitable for intact protein mass analysis up to 250K (mass resolution expected to be ±250 ppm).
  •   Analysis of DIGE protein spot digests with a sensitivity of ∼250  attomol routinely.
  •   Comparative MALDI-MS mapping of control versus experimental digests.
  •   MS and MS/MS analysis of beta peptides.
  •   A variety of biomolecules can be analyzed including oligosaccharides, and gangliosides.
  •  Best suited for simple protein mixtures of 1-3 proteins. More complex mixtures are analyzed by LC-MS/MS  using either a single or MudPIT run.