What is our policy for charging users?

The Proteomics Core has a simple charging policy:

1. No samples will be prepared or run until the information has been entered into our sample submission site.
2. We charge for every sample run, regardless of whether an expected result is obtained. The only exception to this rule is where processing or instrument problems in the core have caused the lack of result.

Why do I have to pay for samples that deliver no useful result?

Many users are confused why we charge for samples that deliver no useful result. Regardless of whether the result expected is obtained we incur costs for sample preparation and MS / staff time and consumables. We run QC samples regularly on our MS instruments so we can ensure failures are not due to instrument problems. In addition service samples are processed and run in batches. We can identify failed sample processing where problems occur across the batch of samples.

Failure to identify a protein from a gel band can be due to many reasons. The most common is simply lack of enough protein to detect by mass spec. Difficulties can include:

• Not all proteins digest with trypsin into peptides that ionize well, and are observable easily by MS.
• Some proteins cannot be recovered easily from gels, limiting the amount that is available in the solution injected for analysis.
• Samples can be contaminated before reaching the core, in ways that hinder extraction of protein from the gel, or affect the MS run.
• Proteins can be modified – we can’t identify modified peptides unless we are looking for the correct modification.

We can never guarantee protein identification from a gel band. For coomassie stained gels we can generally identify proteins, due to the large amount of protein present in the band. Silver-stained gels can fail to produce an ID, since even though the protein is visible with the stain there may not be enough present to see by mass spec. This is especially the case if the protein sequence does not give easily observable tryptic peptides, or there is some contamination or use of a non-MS compatible staining protocol. In some cases we can advise on the likelihood of identification, where the protein is known or suspected in advance of MS. We can never guarantee the identification of an unknown protein from a gel band.