Protein Identification

Identify your proteins and peptides by mass spectrometry

Are you looking for a fast and reliable service for identification of the proteins /peptides in your solution or the bands in your gel?

Where the peptide map is compared to public or custom databases?

Along with the physiochemical properties and link to the database entry, you also receive the obtained sequence coverage maps – where peptides, use...

Are you looking for a fast and reliable service for identification of the proteins /peptides in your solution or the bands in your gel?

Where the peptide map is compared to public or custom databases?

Along with the physiochemical properties and link to the database entry, you also receive the obtained sequence coverage maps – where peptides, used for identification, are highlighted in the sequence.

PROTEIN

Protein Identification using mass spectrometry is a very powerful and versatile tool. Especially since you can use our service to identify or verify a single protein. However, you can also identify multiple proteins in complex samples. The analysis works equally well for both in-gel samples or in-solution samples. The service consists of a digest of protein material using a protease, followed by MS and then MS/MS sequencing.

The protein identification is made by matching the obtained data to the reviewed public protein database from Swiss-Prot.

PEPTIDE

It is also possible to perform peptide identification by MS and MS/MS sequencing. Our analysis works only for in-solution samples. To get an accurate identification of the peptides in your solution, we search the acquired MS data against the SwissProt or UniProtKB databases.

Do you need high-throughput protein identification service of many samples? Or do you need to search against a custom database?

Then please send us a project proposal request. We will get back to you within 24 hours.

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What electrophoresis gel types can I use for MS protein identification?

The most commonly applied type is the polyacrylamide gel. The protein separation can occur within one dimension, as in SDS-PAGE where proteins are separated by mass, or in two dimensions, as in 2D-PAGE where proteins are separated by isoelectric point in the first dimension and by mass in the second. All standard gel types for protein separation can be used in combination with in-gel trypsin digestion and MS-analysis to identify the separated proteins.

What gel staining methods can I use for protein identification analysis?

Coomassie blue is a non-covalent dye used for post-electrophoretic staining, all different types of Coomassie blue can be used for protein identification analysis. Silver staining, with silver nitrate or silver diamine, has a higher sensitivity than Coomassie blue, but the chemicals used might affect the MS-based protein analysis in some protocols. Optimized silver staining method for MS analysis can be found in our protocols (at the Support menu). More recent dyes are fluorescent such as Sypro Ruby and Deep Purple that are also compatible with MS protein identification.

How much material is needed to identify the protein?

For protein identification analysis really good data are obtained with clear Coomassie or Silver stained bands, e.g. with 50 femtomole or more loaded onto the protein gel. Look into our Protein Analysis Blog for more information.

What is Keratin and how do I avoid contamination of my sample with Keratin?

Keratin is a naturally occurring protein found in e.g. hair, dead skin, latex gloves, DTT, buffers and wool clothing. It is important to minimize keratin contamination by wearing a lab coat and non-latex gloves. Additionally, everything in touch with the gel should be free of dust, e.g. by being washed with 70% ethanol. The in-gel digestion must be performed in a clean work area like a laminar flow hood. Additional information is found in our Protein Analysis Blog.

Who is this for?

We primarily help customers within the pharmaceutical industry, and biotechs working on drug development, e.g.

Project managers

Working with process development and characterization projects.

Analytical experts

Protein scientists that work with elisa, masss spectrometry, or CMC.

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