PTM Site Identification

Our PTM site identification service covers Acetylation, Methylation and other PTM sites. The PTM site identification workflow is ideal for purified proteins or IP samples with target proteins enriched. Each experiment covers the identification of 1 type of PTM site in a single protein per sample. Customers can send in-gel or in-solution samples, and provide the amino acid sequence or accession number of the target protein.

The presence of a PTM site is shown by MSMS spectrum, highlighting the modified b or y ions as well as a precursor peak showing the signature ion (if present).

Main services offered:

  • Phosphorylation is the most studied PTM. Our phospho-site Identification service covers all 3 amino acids (S, T, Y). This involves enriching phosphorylated peptides followed by liquid chromatography and targeted mass spectrometry.
  • Acetylation mainly occurs on Lysine. Acetylated-Lysine is a reversible PTM of proteins and plays a key role in regulating gene expression. Our acetyl-site identification service covers all acetylated Lysine sites in a single protein.
  • Methylation mainly occurs on Lysine & Arginine. Protein methylation has been studied mostly in histones. Methyllysine or Methylarginine on certain residues in histones can repress or activate gene expression. Our Methylation-site identification service covers all mono-methylated Lysine sites in a single protein per sample. We also offer the option to include Arginine methylation as well as dimethylation.
  • Other PTMs, such as Ubiquitination, Glycoslyation, Citrullination and others are also covered by our service.

PTM Site Identification Procedure

Gel Bands/Spots or In-Solution Samples

Procedure: step 1: cleaning and buffer exchange of in-gel or in-solution samples

Reduction/Alkylation & Trypsin Digestion

Procedure: step 2: Reduction, alkylation & trypsin digestion

NanoLC-MSMS targeting PTM peptides

Peptide spectrum containing the PTM Sites

MSMS spectra showing b and y phosphorylated ions

Sample Info

Sample type: We accept in-solution, in-gel samples, or IP beads for this service.

Required information: Amino acid sequence or accession number of the target protein.

Protein amount: 2-20 µg of purified protein or protein mixture with target proteins enriched (such as IP).

Protein concentration: 5-20 mg/ml is preferred for in-solution samples.

Buffer: Please feel free to submit samples in whichever buffer that you would normally use.  Please inform our scientists about the buffer composition. Additional charge may apply on samples that require extensive amount of the extra work such as protein eluting, concentrating, buffer exchange or serum abundant protein depletion.

Biohazardous Materials: We do NOT accept samples containing any biohazardous materials. If your samples contain any biohazardous materials, please make sure to deactivate them completely using the appropriate procedure and declare them in the order form. In addition, we do NOT accept any samples containing Level 4 biohazardous materials even if they are deactivated. Please refer to this page for the rank of biohazardous materials.


Services DescriptionAcademic/Governmental LabsIndustrial/Commercial Labs
Identify all sites of a single PTM323A$895323N$995
Manual inspection of MS/MS spectrum202A$130 / hr202N$145 / hr

Each order should have a minimum of 2 samples. Turnaround time is 5-7 business days. Price covers the identification of all sites of 1 type of PTM for 1 protein per sample. Call to inquire about identifying additional types of PTMs. Following are the major steps:

  • Reduction and alkylation
  • Trypsin digestion
  • Peptide extraction
  • Desalting
  • Targeted NanoLC-MS/MS on PTM precursors based on in silico digestion
  • Search against target protein sequence with PTM
  • Data report:
    1. Top hits
    2. List of all matching precursors with and without PTM sites

Price does NOT cover:

  • Protein identification
  • Sample preparation
  • Data request in addition to the standard report such as MSMS spectrum

If a customer does not provide protein sequence or accession number, an additional fee will be charged for protein identification.