WHAT MATTERS IN CLINICAL PROTEOMICS? 2. THE NEED FOR STANDARDIZATION

By Nicolai Bache

Many areas in clinical proteomics could benefit from a broader adoption of liquid chromatography mass spectrometry (LC/MS) methods.  What needs to be done to make LC/MS a standard technique in the clinic?

To find out, we asked the experts: scientists working on clinical proteomics projects day in and day out. More than 70 scientists took the time to respond – group leaders, postdocs, students and engineers, working in academia, industry, and hospitals all over the world.

LC/MS APPLICATIONS: AN EVER-GROWING LIST

First, we were curious about what scientists are doing. That is, for which applications do they use LC/MS? The outcome was a long list, ranging from protein identification and quantification, which are carried out in almost all labs, to niche applications such as human leukocyte antigen (HLA) identification and peptidomics (Fig. 1).

Fig. 1: A broad range of proteomics applications are addressed by LC/MS. 
(Question: Which application field(s) best describe your work?)

Adding up the numbers, it is clear that each lab performs more than one application. In fact, 80% of labs use their LC/MS instrument for three or more different applications. Technology improvements and easier handling have certainly led to a wide recognition of the utility and versatility of LC/MS for proteomics studies.

STANDARDIZATION IS KEY

Next, we wondered how LC/MS experiments are future-proofed. As new methods are continually developed, how do users make sure their procedures stand the test of time? More than half of the respondents count on standardized and published protocols, rating them the most important tool to stay up to date with new developments (Fig.2). Especially with the increasing diversity of applications, procedures need to be compatible with many sample types and scientific questions.
Many users combine vetted protocols with commercially available sample prep kits and a careful choice of software. Some respondents future-proof their experiments by buying from only one vendor, while others believe it is not worth the effort as things are changing so fast anyway.

Fig. 2: Published, standardized protocols are key to future-proof experiments in large-scale proteomics.
(Question: How do you future-proof your experiment & data?)

Clearly, standardized and published protocols are needed in the clinical setting where any change in protocol requires a lengthy approval procedure. How do users of LC/MS techniques stay abreast of new protocols and developments? Most of them prefer to learn by reading scientific journals and by attending conferences. Word of mouth is also important for many – probably including off the record discussions at scientific meetings. Less favored are websites, newsletters, and social media. Therefore, a protocol published in a peer-reviewed journal and presented at a scientific meeting is most likely to become adapted by other labs as a standard method.

We believe that establishing standardized, future-proof protocols is key to increase the adoption of LC/MS in clinical proteomics. Evosep facilitates this process by boosting the robustness and speed of liquid chromatography and sample preparation. Read more about the results of our survey in “What matters in clinical proteomics? 1. Challenges of large cohort studies”

Evosep standardizes and future-proofs LC/MS methods.

 

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