Conclusions
The focus of proteomics research has started to shift from qualitative protein identification to a more targeted quantitative approach for monitoring specific proteins or pathways. Targeted protein quantitation is a demanding application. Success depends on many factors, a critical one is building selected-reaction monitoring (SRM) methods that provide excellent specificity and sensitivity.

The novel Pinpoint software facilitates the transition from qualitative proteomics to targeted protein quantitation. It includes an extensive array of tools for hypothesis- and bioinformatics-based building of SRM methods. Pinpoint software has the unique ability to use previously acquired spectral libraries from LTQ ion trapbased discovery experiments to build robust SRM methods more quickly. In addition to method building, Pinpoint software provides numerous verification tools to assess data quality at the transition, peptide, isoform, and protein levels using pre-defined criteria. The scoring results at each level enable automated method refinement to rapidly create verified methods with the ultimate goal of future clinical assay validation.

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