PTM Identification

Introduction

The presence or absence of post-translational modifications (PTMs), such as phosphorylation, on a protein are often as interesting as the presence of absence of the protein itself. The PTM ID service offers identification of PTMs on a protein from a strong coomassie band, or an in-gel mixture.

A strong coomassie band is required to get good sequence coverage of the proteins. If we don’t see a region of sequence we cannot identify PTMs on that sequence. The standard protocol uses tryptic digest, but this will not give complete coverage of a protein. It may be neccessary to digest with alternative enzymes to gain optimum coverage of the protein, and maximize the chances of identifying a PTM. It is possible to somewhat predict sequence coverage – contact us!

We do not manually identify PTMs, but instead search acquired MS data for PTMs of interest specified by the customer. We offer to identify common PTMs such as phosphorylation, methylation, acetylation etc. We may consider unusual PTMs where literature demonstrating prior identification by MS using methods similar to ours is available.

What Does it Cost?

Standard Service: $240 per gel band with tryptic digest, or $280 with alternative digest. Each sample submitted must consist of no more than 5mm of gel lane. This service includes identification of a single specified common PTM on a single protein. Certain PTMs may be excluded due to complexity of analysis. Contact the core for information.

Custom service: Standard service + $60 per hour data analysis. Custom service supports mapping of multiple specified PTMs, on multiple proteins, and within complex mixtures. Also unrestricted search for multiple PTMs. Base price includes up to 30min data analysis time. Contact core for an estimate of cost.

Free training: Custom PTM analysis uses a lot of staff time, so we offer free training to lab members who want to perform data analysis themselves using our analysis pipeline. Contact the core for details.

What We Do

We run your gel band samples on our Q-Exactive or Orbitrap Elite mass-spectrometry platforms, using a short reverse-phase LC-MS/MS method. We identify proteins from samples using our in-house data analysis pipeline (CPFP). We search for PTMs that you have specified. We run a PTM localization scoring algorithm against the data. We provide a brief summary of results, and access to full results online. We are available to discuss results with you.

What You Must Do

To submit a sample for PTM ID you must:

  • Contact us if you are concerned about sequence coverage, or want to look for PTMs at a certain location in your protein.
  • Resolve your protein of interest on an SDS PAGE gel.
  • Stain your gel with Coomassie Blue.
  • Ensure the band of interest is a strongly stained band.
  • Cut out the band of interest following our guidance carefully.
  • Ensure your band is no larger than 10mm of gel. The closer you can cut around a band the better.
  • Slice the band into 1mm cubes – this is very important to maximize recovery of material from the gel during sample processing.
  • Place the sliced band into an Eppendorf 1.5ml tube, which has been rinsed with 50% organic solvent and millipure water.
  • Follow the general guidelines for sample submission.
  • Ensure you provide information regarding the PTMs you wish to attempt to identify.

Sequence Coverage Limitations

We can only identify a PTM in the region of a protein observed by MS. The mass spectrometer can only see peptides with length between approx 7 and 25 amino acids, that have a sequence that allows them to ionize well. Tryptic digest typically results in as little as 20% coverage, or as much as 80% coverage for a protein from a strong coomassie band. Coverage is dependent on the sequence of the protein – does it produce good tryptic peptides? Multiple enzyme digests can be required to cover a large amount of the protein sequence, or even a moderate amount of sequence for difficult proteins.

It is always beneficial to consult the core before submitting a PTM sample. Is complete coverage neccessary? Are we likely to observe PTMs in a particular region of interest? These kinds of questions should be asked early to avoid unnecessary submissions and expense.

Other Warnings & Limitations

PTMs can affect the way peptides fly in the mass-spectrometer, and this along with other reasons can make them difficult to identify.

MS/MS spectra that show the sequence of a peptide are often incomplete, and it is not possible to confirm the exact location of an identified modification. In addition various modifications have very similar masses, and it can be complex or impossible to distinguish between them.

Thorough PTM mapping of a protein is time consuming. We will work with customers to maximize the results of PTM experiments, within the confines of staff-time that are present in a core facility.

Any Questions?

If you have any questions please contact ProteomicsCore@UTSouthwestern.edu before you prepare and submit your samples.

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