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Biogenity's complete workflow for your proteomics study using LC-MS


June 1, 2021 | By Louis Loeb

At Biogenity, we are very proud to be able to facilitate your proteomics project using Mass Spectrometry. Since we have not posted on our proteomics workflow, we thought it would be obvious to present the whole customer journey, highlighting how to support your next project from sample to biology.

Starting with the initial consultation

Everything starts with the initial request and consultation. Upon every request, we always offer a free consultation to discuss the focus of the study, which is essential to align the method to the aim. The initial consultation is vital, as the scientific discussion tributes to a shared understanding of essential aspects of the project. In these meetings, we also provide:

  • All different approaches that can be used.
  • The difference in expected results.
  • Demands regarding sample and budget.

  • This allows identification of any limiting factors to be considered when generating a project, which saves you time and ensures the most value from the results.

    After the consultation, both Biogenity's project manager and the client have a much deeper understanding of the project. We then formalize the project, a quote, and the necessary contracts. If you like, we can also give several estimates dependent on sample size and methods chosen, e.g., one where we go for the deep proteome and another with a budget in mind. Here, we will be able to discuss the pros and cons of each. When a project has been agreed upon, the laboratory is ready to receive the samples and initiate sample preparation.

    Specialists in the laboratory for proteomic Mass Spectrometry

    Our colleagues in the laboratory are specialists in all the different aspects of working with Mass Spectrometry, ensuring that your samples are in great hands. One of the things that make our laboratory exceptional is that we have state-of-the-art equipment with the latest models from Thermo Fisher, including the Eclipse and the Exploris 480, which set the threshold of what is detectable today. We use off-the-shelf parts for the equipment, meaning that if something is broken, we can take a new part from the shelf and replace it, making the analysis highly reproducible.

    Your own data scientist

    Data analysis is where it all comes to shine. Biogenity's data analysis is much more than simply a data analysis. It offers an insight into what biology is, e.g., potentially activated or deactivated in the different conditions, without the hassle of postprocessing the data. Our team does it all: data filtration, outlier testing, variance plotting with PCA, clustering, and the statistics - and that is just with the Statistical Data Analysis.

    We also do bioinformatics, where we look for pathways, biological processes, molecular functions, and cellular components, which can have relevance in the data, including enrichment analysis, comparative figures, and network mapping hereof.

    Set all the regulations into perspective

    Bioinformatics takes the regulations and puts them into perspective, which biological pathways or biological processes are potentially up or down-regulated. Can we see some molecular functions come into play, and are there particular cellular compartments affected? This all gives a good explanation or suggestion to explain what is actually happening in the different conditions.

    If you would like to try our Bioinformatical data analysis, you can download our test sample here:

    Download PDF report + figures and tables

    (File size: 355 MB. File type: .zip)

    Download PDF report

    (File size: 25 MB. File type: .pdf)

    Biological modeling on strong trends

    We also perform biological modeling, where we can see that strong trends can be modeled, thereby creating a model that might predict which conditions are present. It could be the disease or a responder and a non-desponder to a treatment. The modeling is a tailored solution, and it's also only available with +50 samples within only a few conditions. If we have more conditions, we need more samples, and the more samples there are in the analysis, the better is the chance to find a good model.

    What do you get in the end?

    Biogenity makes the complex data into a simple overview so that you can focus on the biological question. We deliver a report explaining the results and all steps in the data analysis with full transparency. Our rapport is made so that it can be shared in research groups, consortiums, and with management so everyone can get an overview of the discoveries and understand the content of the analysis. If you haven't already experienced our data analyses, we should mention that you also get vector-based figures ready for a presentation and articles. You will also receive tables of all the results from regulations to unique identifications, outliers, etc.


    The post-consultation is a meeting that we plan after you have received the final report to answer all the questions that might be. We experience that the questions can be from just the individual processes to the actual statistics and bioinformatics that we are seeing. Sometimes a new or follow-up experiments may appear from the consultation. But this meeting is deliberate in answering all the questions you might have, making sure that everything is transparent and that you as a customer understand every part of that data.

    "The most important part for me is that I feel comfortable that the client got full value from the analysis." - Kenneth Kastaniegaard, CEO at Biogenity

    Sometimes, you would like to have a helping hand or a third-party validation when interpreting the data. For this, we have our highly specialized consultant, who is relevant in different aspects.

    Professional consultation for interpretation of biological findings

    Suppose you want to have a fast answer to a specific aim where some biological interpretation is involved. In that case, our consultant will then take the data analysis, go through what was brought forward, and then compare it to the literature or the study aim, and give a discussion and maybe even a conclusion on the topic. The consultant is also an excellent way to know how can the results of this analysis be validated. Our consultant can also advise you on how your research should be published, where it could be published, and what to include. This is, of course, not always relevant. Sometimes the client is the actual expert. Other times, the data analysis is giving a clear enough result to interpret directly from the aim. Nevertheless, it is always great to have the option to include professional consultation for the interpretation of biological findings.

    Are you starting a proteomic study or just considering it? Then contact us. We are happy to set up a free introductory meeting to discuss your proteomics project in detail. Contact us directly at (+45) 71116050 or use our contact form.

    Kind Regards,
    The Biogenity Team