Proteome Factory offers protein identification exclusively by LCMS-based high resolution mass spectrometric techniques. This ensures highest sensitivity for detection of minute protein amounts. Excellent mass accuracy delivers high confidence results allowing unequivocal identification of one and more proteins within a sample. Results will be provided electronically in a pdf report including protein name, amino acid sequence and molecular weight.

Depending on sample complexity we offer services using different nanoHPLC-ESI-MS/MS instrument time.

  • Short gradients are for analysis of 2-DE gel spots and protein bands from SDS-PAGE containing single proteins.
  • Normal gradients are fine for protein complexes and low to medium complex protein samples. This is also designed for the analysis of dissolved proteins in solution.
  • Long gradients for profiling of highly complex protein mixtures are available. We provide label-free quantification (LFQ) for comparative analyses of complex samples.

Please share information about the samples and the aim of the analysis. Depending on this information we can choose appropriate databases and give guidance to appropriate threshold parameters. Keep in mind: protein identification by database search is a qualitative technique, but with additional data analysis some information about protein abundance can be obtained.


Sample formats

Samples can be submitted as protein gel bands, protein gel spots, lyophilzed, or in solution. 

Gels are preferrably stained with Coomassie. When silver staining is used, be sure to apply a dedicated MS compatible protocol. For proteins in solution and for lyophilised samples please avoid large amounts of detergent and note the buffer composition on the submission form. 

We provide

Samples are cleaved with trypsin followed by online separation and detection with LCMS. MS/MS spectra are submitted to database search against NCBInr or Swissprot.  

You receive

A result report of protein identification will be send by email as a pdf document containing the results of protein database search. We can also provide reports via SSL server.

How to order

Send your samples together with the completed sample submission form for protein identification to us. Information below is provided about sample requirements and shipping. Please notify us via email or phone of your shipment. 

Pricing (effective 1st October 2023)

Prices in EUR

(per spot/band/sample)

Short gradient Normal gradient Long Gradient
1 sample 300 550 850
2 - 9 samples 250 500 750
10 - 24 samples 225 450 650
25 and more samples inquire inquire inquire

Turnaround times are 7-10 days. Express services are available: 2-4 days plus 50% surcharge, overnight express plus 100% surcharge. Please contact us to arrange priorisation of highly urgent samples.

Depending on your analytical question add-on services for sample preparation and data analysis are feasible:

  • proteolysis with trypsin, Lys-C, Lys-N, chymotrypsin, Glu-C, Asp-N and more
  • deglycosylation by PNGase F for removal of N-linked glycans
  • setup of specific database from customer-supplied FASTA file
  • de novo peptide sequencing with BLAST search
  • manual data evaluation (150€/hour)

Have a look at our Knowledge Base to find our how to prepare samples for best results.