Sample submission

A general note

We regard it as our job to help you tackling your experimental question in the best possible and most effective way. We will treat your samples with utmost care and apply the most sensible procedures existing to our knowledge to provide you with the information that you need. Despite these efforts we cannot guarantee that all analyses will turn out to be successful. Apart from technical problems (contamination by keratins, detergents, etc.) which we try to avoid, it is still possible that your peptide or protein of interest cannot be identified because it is below the detection limit or because it has properties which are not suitable for mass spectrometry. If such a situation occurs we consider it important to take the time to explain what the difficulties are and to see if we can find another solution together. This means whenever there is a problem, when there is something that is not clear to you, or when you have just a really interesting idea in mind that you would like to have feedback on, please contact us or just drop by in our office – we consider this an important part of our service and by no means a “disturbance”.

 

Sample submission for intact protein mass determination

  • You can submit intact protein mass samples every Wednesday in our facility from 9:30-16:00. For all other applications please see below.
  • If your sample can be stored stably at 4°C or -80°C you can submit your sample earlier during the week.
  • If there is high demand further service days will be introduced.
  • Please have a thorough look on our sample preparation guidelines for intact proteins to avoid the most common problems
  • Please fill out the submission form for intact mass and send it via email.
  • Result turnaround time: approximately 2-5 workdays, for standard samples, depending on workload.

 

Sample submission for all other samples

Submission schedule and turn-around times

Please always contact us before submitting samples so that we can plan our workload accordingly. We will then let you know when the samples can be submitted and also give an estimate when they will be processed. Standard samples for simple workflows (like gel IDs) can be submitted after short notice, for all other samples (e.g. CoIPs on beads, etc.) please inform us at least three days in advance.

When submitting samples which are important to be processed immediately (for example samples on beads) please consider that sample processing before digestion takes a couple of hours, followed by an overnight digest and subsequent steps the next day. Consequently, such samples should not be submitted after 2 pm and not on Fridays or before holidays.

We aim to return data within 7 to 10 workdays. However, turnaround times certainly depend on the length of the sample queue and the complexity of the analysis, we will try to give a decent estimate for this during submission. Standard workflow samples are processed in the order of their arrival. We will not prioritize samples from specific users.

Sample submission

To maximize the number of successful measurements, please consider the following points before submitting your sample:

  • Please download and complete the submission form and send it to us on the day of submission. It is in your own interest to provide as much information as available about the nature of the samples and about your requirements. The more we know about your sample the easier it is to choose the best suited workflow and to avoid common problems.
  • Please have a thorough look on our sample preparation guidelines to avoid the most common problems or contaminations.
  • In case of samples separated by gel electrophoresis, please provide a scan of the stained gel with the submitted bands/spots labeled. You can excise bands or spots yourself before submission or bring the gel to the facility and excise them with our help.
  • In case of samples in solution, it is important for us to know the exact composition of the solvent and the amount or concentration of the protein. If possible please run a gel with a small aliquot of the sample and submit a photo or scan of it.
  • Label your sample tube with a permanent marker. The label should contain the name of the sample owner and a short identification number or code that allows unambiguous identification for you and us.
  • For the identification of proteins derived from constructs please include the exact sequence, including tags, cleavage sites, etc. which you expect to be present in the protein in the submission form or send it as a separate file.
  • To make sure that we do not harm our LC-MS system and to estimate the injection amount we run a small fraction of each sample on a QC system beforehand. We reserve the right not to measure particular samples if the QC system indicates a contamination with problematic substances.
  • Radioactively labeled samples must not be measured on our systems and cannot be accepted. 
  • 15N-labeled proteins are not suitable for routine analysis. The increased complexity of the isotopic envelope and incomplete labeling, make peptide identification from these samples quite challenging. Please contact us if you would still like to work with 15N labeled proteins.

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