Protein identification

Our protein identification service has been running for over 10 years and is internationally known for providing reliable, high-confidence results with short turnaround times.  The service is run weekly with results typically provided by the end of the week following receipt of samples – if not sooner.  The service accepts SDS-PAGE bands, 2D gel spots and proteins in solution, and includes:

  • Destaining and digestion with trypsin
  • MS/MS of up to 10 peptides per sample
  • Mascot database search and results report

Mass spectra will be matched to the NCBI non-redundant protein database, or another in-house database if requested.  If alternative database searches are required, such as sample specific EST datasets, this can be arranged on an individual basis.  MALDI-MS and MS/MS are performed using a Bruker ultraflex III MALDI-TOF/TOF, which allow us to obtain higher-confidence identifications by including tandem spectral data in Mascot searches.  

For more information, please see our FAQ or contact us.  Please see here for prices.

De novo sequencing

Database matching with raw mass spectral data cannot always identify a protein, for example, when the protein sequence is not contained in the database being searched. In this case, amino acid sequence can be obtained by de novo sequencing of MS/MS spectra of peptides. The amino acid sequence can then be used with a specialized BLAST search program called MS BLAST or in a Mascot sequence query.

We offer a de novo sequencing service, in which software-generated peptide sequences are verified by manual inspection of the MS/MS spectra. The cost of de novo sequencing starts at £500 with bulk discounts available, which includes sequencing and searching of the three best peptide spectra produced from the sample. This charge does not include sample preparation or acquisition of mass spectra, and should be added to the charge for protein identification shown above. Further details regarding de novo sequencing can be found in our FAQ.

Please note that not all peptides in a mixture will be observed by MALDI-MS, which means that the percentage of total protein sequence accounted for is never 100%. LC-MS can help to reveal more peptides and thus increase sequence coverage. Our shotgun proteomics service can be used to increase coverage.

The standard identification procedure can provide highly confident protein identification but is unlikely to be able to confirm terminal sequence.  If terminal sequencing is required, we typically do this by MALDI-ISD. For example, please see here.

Protein identification prices

Prices shown exclude VAT.

Commercial customers please add 75%. 

Number of samples£ per sampleTotal charge (£)
1 100.00 100.00
2 75.00 150.00
3 66.67 200.00
4 62.50 250.00
5 58.00 290.00
6 55.00 330.00
7 52.86 370.00
8 51.25 410.00
9 50.00 450.00
10 48.00 480.00
11 46.36 510.00
12 45.00 540.00
13 43.85 570.00
14 42.86 600.00
15 42.00 630.00
16 41.25 660.00
17 40.59 690.00
18 40.00 720.00
19 39.47 750.00
20 39.00 780.00
25 36.80 920.00
30 34.00 1020.00
35 32.00 1120.00
40 30.50 1220.00
45 29.33 1320.00
50 28.40 1420.00

Proteomics Right Col Img

Bruker 9.4T