Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.

Establishing the fitness for purpose of mass spectrometric methods.

This report is submitted by a working group sponsored by the ASMS Measurements and Standards Committee. The group responded to a 1998 opinion piece dealing with mass spectrometry in trace analysis (Bethem, R. A.; Boyd, R. K. J. Am. Soc. Mass Spectrom. 1998, 9, 643-648) which proposed that the concept of fitness for purpose addresses the needs of a wide range of analytical problems. There is a need to define fitness for purpose within the current context of mass spectrometry and to recommend processes for developing and evaluating methods according to suitability for a particular purpose. The key element in our proposal is for the interested parties to define in advance the acceptable degree of measurement uncertainty and the desired degree of identification confidence. These choices can serve as guideposts during method development and targets for retrospective evaluation of methods. A series of more detailed recommendations are derived from basic principles and also from reviews of current practice. This report highlights some areas where consensus is evident, but also revealed the need for further work in other areas. The recommendations are aimed primarily for the laboratory analyst but we hope they will be accessible to the non-scientist as well. Our goal was to provide a framework that can support informed decisions and foster discussion of the issues, because ultimately it is the responsibility of the analyst to make choices, provide supporting data, and interpret results according to scientific principles and qualified judgment.