Speedy and detailed protein ID of SDS gel bands

Jun 9. 2020


Can I identify hundreds of gel bands in a few days?

The biopharmaceutical company that I work for, consistently uses SDS PAGE and Western Blotting to check protein expression. But this means we spend a great deal of money on antibodies, which I feel may be unnecessary. In addition, there are several unknown proteins in the gels, possibly degradation products, which we would like to identify.

Is there a fast and reproducible method to identify hundreds of gel bands within a few days?


If you develop or manufacture any type of protein-based biologic, you know it is essential to evaluate protein expression. Both to verify that the biopharmaceutical protein was produced in sufficient amount and to investigate impurities co-produced by the host cell.

The common approach is to rely on one of these standard methods:

  • SDS-PAGE and Western Blotting (WB)


  • SDS-PAGE and In-gel digestion/mass spectrometry

The method that includes WB is fast and easy to run, if you have the antibody needed to recognize the drug product. However, since this approach depends on antibodies and their specificity towards the target protein, there is a degree of uncertainty [1].

Also, you should be aware that you rely on a constant antibody supply – which makes it costly when you have a high number of samples. And it is vulnerable, since you cannot conduct the analysis, if you run out of antibodies. Furthermore, the antibodies (probably) will not cover the degradation products or other unknown proteins, also making the approach incapable of identifying proteins in the sample besides the drug product [1, 2].

protein ID sds gel band

Therefore, it makes sense to apply a method that runs without antibodies – and can take a high number of samples within a short time (hours and days). Some companies thus benefit from protein ID /confirmation by in-gel digestion and mass spectrometry (LC-MS). However, this requires more time than SDS-PAGE and WB – at least for traditional ways of setting up the method [1-3].

Improved speed and lowered cost of running protein ID of gel-bands

Luckily, Alphalyse found a way to bring down the time it takes to identify proteins in large numbers of gel bands using NanoLC-MS/MS: Adding an EVOSEP® one instrument in front of the mass spec instrument, reduces the run time to 25% of traditional protein ID LC-MS. The gradient is simply 4x shorter, without compromising protein detection and identification.

The setup is combined with robotic-automation of the in-gel protein digestion and sample preparation for LC-MS. This results in higher speed, which is one of the biggest advantages compared to standard methods.

Furthermore, the approach overcomes problems with carryover, which is sometimes an issue with traditional LC-MS analysis [1-3]. We can thus increase reproducibility and sample throughput.

Identify impurities and degradation products

You will also obtain an overview of all proteins in your samples – not only confirming the drug product presence. You can even identify process-related impurities, such as residual protein added as part of the process development, or host cell protein that originate from the expression system (CHO, yeast, E. coli, etc.) used to produce the active pharmaceutical ingredient (API).

Finally, 20-80 percent sequence coverage is easily obtained and may be enough to distinguish isoforms and protein/peptide variants from each other. And the approach even identifies degradation products. This is because it does not rely on antibodies, but instead determines all proteins in the sample independently of the process or the expression system.

Let Alphalyse help you with large runs of gels:

With the analysis, you can identify or confirm the protein bands in your SDS PAGE gel – in the fastest and most precise way. The setup is advantageous for hundreds of samples at once, thus saving you countless western blots and exceptional costs on antibodies.

For more information, contact Alphalyse to set up a virtual meeting:

Learn more at a virtual meeting with Alphalyse >>>


[1]          Luque-Garcia et al: “Analysis of electroblotted proteins by mass spectrometry: protein identification after Western blotting“, Mol Cell Proteomics, 2008

[2]          Lahm HW, Langen H.: “Mass spectrometry: a tool for the identification of proteins separated by gels“, Electrophoresis, 2000

[3]          Ranjan AK, Gulati A: “Two-Dimensional Electrophoresis and Mass Spectrometry for Protein Identification“, Methods Mol Biol, 2019

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Alphalyse uses expertise in the field of protein chemistry and bioinformatics, combined with top-of-the-line mass spectrometry equipment, to provide protein analysis services globally.

Alphalyse aims to deliver high quality data and customer service to all of our clients in a fast and convenient way.


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