Frequently Asked Questions

1.      How do I submit my samples?

Please contact the Platform before your experiment. We provide a free consultation to understand your experiment and design the best approach based on your needs. We will also discuss the feasibility and expected outcomes and coordinate the sample submission.

2.      Do I need previous knowledge to perform a proteomics analysis?

You do not need previous knowledge. We provide expert advice and support for your projects from experimental design to data analysis and presentation. If you are interested, we organize workshops and offer training to individuals upon request.

3.      What do I need to consider when I prepare my samples?

Be aware of common contaminants that significantly interfere with mass spectrometry measurements and reduce the quality of your data. For example, polyethyleneglycol (PEG) and detergents containing PEG (e.g., Triton X-100, Tween, NP-40).

For gel band samples, Commassie staining is suggested. Please wear clean gloves and leave blank lanes in between samples to minimize cross contamination. Please wash the gel extensively after the run to remove the SDS as much as possible and store the gels in clean containers.  

4.      How long does the analysis take?

Requests are taken on a first-come, first-served basis. The estimated timeline depends on the current workload, number of samples and depth of analysis and it will be communicated upon submission of the samples.

5.      How much does it cost?

The cost largely depends on the experimental design. We can provide you with an indicative quote after the initial discussion of the project.

6.      What kind of data will I get?

This is largely dependent on the goal of your project. For identification, we provide the list of proteins that are detected in your samples. For quantification, we usually provide you with the data matrix containing abundance of each protein in each sample, as well as the list of significantly changed proteins between sample groups. We also offer a variety of additional analysis upon request.

7.      Does the Platform provide training?

Yes. We organize workshops and upon request, we provide training for those who are interested in participating in any stage of their project, from sample preparation to data interpretation.

8.      Why could you not identify protein A in my sample?

There are several reasons why a specific protein is not detected:

·       The protein is present at low abundance

·       The protein has poor solubility, leading to their loss during processing

·       The protein is not in the database

·       The protein might degrade during sample preparation

·       The protein is protease resistant or does not contain enough cleavage sites for trypsin, thus generating not enough detectable peptide, or it has too many cleavage sites, resulting in peptides that are too small to be detected.

·       The protein has extensive post-translational modifications (PTMs), which alter peptide masses and fragmentation patterns, making identification challenging

9.      I expect to see 1 protein from my gel band, why do I get dozens of proteins?

Several reasons can explain why we identify multiple proteins from a single gel band:

·       The protein of interest is part of a protein complex

·       The band contains proteins with similar molecular weights

·       Mass spectrometers are highly sensitive and detect even trace amounts of other proteins

·       Contamination from neighboring bands/samples or during sample preparation. Please maintain a clean work environment and leave blank lanes in between samples to minimize protein diffusion and cross contamination. If necessary, use gradient gel to better separate proteins with similar molecular weights.

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