The Laboratory routinely performs qualitative analysis of protein samples of various complexity - from pure proteins to complex mixtures. 

The standard procedure for qualitative MS analysis of a protein sample includes following steps:

  • reduction and alkylation of protein disulfide bonds, followed by tryptic digestion to obtain peptide mixture;
  • liquid chromatography (LC) separation of a sample, MS measurement of peptides and their fragmentation spectra (tandem mass spectrometry);
  • searching of acquired spectra against; a protein sequence database of choice (NCBI, UniProt or customer-supplied database) using Mascot search engine (, followed by validation and formatting of results.

There are some limitations that follow:

  1. Only proteins present in the database used for Mascot search will be identified.
  2. Since a routine identification is performed through comparison of experimentally obtained data with a set of known amino acid sequences, a de novo analysis of a protein (or peptide) amino acid sequence is generally impossible.

The types of samples we routinely perform qualitative analysis on are:

  • gel bands - stained either with Coomassie or silver,
  • pellets,
  • protein solutions - if you are planning to send a solution to us, please read the relevant FAQ section first.

Analysis of other sample types, such as nitrocellulose membranes or proteins bound to magnetic beads is also possible. In such cases, the preparation protocol needs to be consulted with our staff in advance in order to ensure compatibility.

Information on the status of analysis and details concerning data access will be sent to the email address provided in the request form.

Standard qualitative analysis is performed as a service and can be ordered online through our order processing system (