Comprehensive proteomic analysis of protein changes during platelet storage requires complementary proteomic approaches

BACKGROUND: Proteomics methods may be used to analyze changes occurring in stored blood products. These data sets can identify processes leading to storage-associated losses of blood component quality such as the platelet (PLT) storage lesion (PSL). The optimal strategy to perform such analyses to obtain the most informative data sets, including which proteomics methods, is undefined. This study addresses relative differences among proteomics approaches to the analysis of the PLT storage lesion. STUDY DESIGN AND METHODS: Changes to the PLT proteome between Days 1 and 7 of storage were analyzed with three complementary proteomic approaches with final mass spectrometry analysis: two-dimensional (2D) gel electrophoresis/differential gel electrophoresis (DIGE), isotope tagging for relative and absolute quantitation (iTRAQ), and isotope-coded affinity tagging (ICAT). Observed changes in concentration during storage of selected proteins were confirmed by immunoblotting. RESULTS: In total, 503 individual proteins changed concentration over a 7-day storage period. By method, a total of 93 proteins were identified by 2D gel/DIGE, 355 by iTRAQ, and 139 by ICAT. Less than 16 percent of the 503 proteins, however, were identified by not more than at least two proteomic approaches. Only 5 proteins were identified by all approaches. Membrane protein changes were not reliably detected with 2D gel/DIGE methods. CONCLUSION: Although proteomics analyses identified many storage-associated protein changes, these varied significantly by method suggesting that a combination of protein-centric (2D gel or DIGE) and peptide-centric (iTRAQ or ICAT) approaches are essential to acquire adequate data. The use of one proteomics method to study changes in stored blood products may give insufficient information.