Sample Guidelines and FAQs

50 µgTotal protein per sample is comfortable. Results are possible from less than 10 µg.
10+Samples per project. Smaller sets can be bundled with colleagues.
1 weekTo process samples after they arrive, then a 2-4 week queue at the service provider.
5-6 / ~30Biological replicates for cell lines, and for human samples.

Samples

Preparing and Sending Samples

What sample types do you accept?: Provisionally, all sample types. We confirm that your samples are suitable when we discuss your project.
How much starting material do you need?: About 50 µg of total protein per sample is a comfortable amount. We have generated results from less than 10 µg, so talk to us if your material is limited.
How should samples be prepared, stored and shipped?: This depends on the experiment. We'll recommend how to prepare, store and ship your samples based on the sample type and the protocol we agree on, including any buffers or detergents to avoid.
Do you accept samples from outside Cape Town?: Yes. We have processed samples from across South Africa, other African countries, the European Union and the USA.
Do you accept human clinical samples?: Yes, including samples from clinical trials. Ethics approval and Material Transfer Agreements are the client's responsibility.

Analysis

Which LC-MS instrument do you use?: Primarily a Bruker timsTOF HT coupled to an Evosep system. We can source other instruments if your project needs them.
What kinds of analysis do you offer?: Our mainstay is label-free quantitation. We also have experience with iTRAQ and TMT labelling, and have helped set up targeted and cross-linking analyses.
Can you work with any organism?: Yes. If your organism isn't in UniProt, we can work with a protein FASTA file that you supply. For poorly annotated species without a FASTA file, we have used Lowest Common Ancestor analysis.
How many biological replicates do you recommend?: It depends on the sample type. For cell lines, 5-6 replicates are typically enough. For human samples, about 30 are needed for statistically significant results.

Timelines and Pricing

How long does it take to get results?: Samples are usually processed within a week of arriving. They are then submitted to the service provider's sample queue, which has a lead time of 2-4 weeks. If your experiment needs specially ordered reagents, we only receive samples once those reagents have been delivered.
How are projects priced?: The same prices apply to every client, so there are no separate academic or student rates.
Is there a minimum number of samples?: Yes, we accept projects of 10 samples or more. If you have fewer, consider bundling your samples with colleagues in a similar position.
How do quotes and payment work?: Once you accept the quote, we process your samples and invoice you when the data is delivered. Projects that need special reagents, such as isobaric tags or internal standards, require a deposit.

Results and Data

What will I receive?: Every file generated during the analysis, from the raw data to the final report. Smaller experiments are delivered electronically. Larger datasets are delivered on an external hard drive, which is for your account. A typical 100-sample experiment produces 1-1.5 TB of data.
Will you help interpret the results? How do you approach co-authorship?: A straightforward protein identification doesn't qualify for authorship. If we develop methods specifically for your project, or explain mechanisms through the data analysis, authorship should be discussed. The test is simple: if the publication couldn't have been written without our intellectual contribution, we should be authors.
How do you handle confidentiality?: Non-disclosure and Material Transfer Agreements are standard for industry and clinical projects. Your legal team provides the documentation.
How long do you keep data and leftover samples?: We don't have facilities to store samples, so unused samples can be returned to you. Because of the volume of data involved, we don't keep data after sign-off. You can return your hard drive to us if you'd like further analysis later.

Working Together

Can you help before samples are collected?: Yes, and we prefer to. Being involved from the start, including study design and grant applications, matters because many projects fail at the desk, not the bench.
Do you offer training for students?: Yes. We bring all the reagents needed and train students in their own lab.

Every project is different. Tell us about your samples and what you want to find out, and we'll recommend an approach.

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