ARS | Publication request: Evaluation of different multidimensional LC-MS/MS pipelines for iTRAQ-based proteomic analysis of potato tubers in response to cold storage

Submitted to: Journal of Proteome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2011
Publication Date: August 16, 2011
Repository URL: http://pubs.acs.org/loi.jprobs
Citation: Yang, Y., Qiang, X., Owsiany, K., Zhang, S., Thannhauser, T.W., Li, L. 2011. Evaluation of different multidimensional LC-MS/MS pipelines for iTRAQ-based proteomic analysis of potato tubers in response to cold storage. Journal of Proteome Research. 10(10):4349-4886.

Interpretive Summary: Potato is the fourth most important staple crop and consumed worldwide on a daily basis. The total value of the U.S. potato crop in 2008 was $3.8 billion. Like many food crops that are harvested during a limited time period but consumed throughout the year, it is necessary to store potato tubers at cold temperatures for prolonged periods to prevent sprouting and reduce post harvest disease losses in order to maintain the tuber quality and provide material for both the fresh market and processing industries. In this study, we employed a comparative proteomics approach to conduct a global study of the phenotype-specific proteome changes during cold storage of potato tubers. We compared two protein separation strategies and evaluated their performance as judged by two different high performance LC/Mass Spectrometry systems. The results indicate that several key proteins important in controlling starch-sugar conversion as well as other proteins change significantly during storage. It is likely that these proteins are involved in cold-induced sweetening, a significant problem to the potato chip and french fry industries (total value $2.1 billion). Our results provide additional insight into the metabolic processes involved in cold-induced sweetening and may provide practical mechanisms to mitigate its impact.

Technical Abstract: Cold-induced sweetening in potato tubers is a costly problem for food industry. To systematically identify the proteins associated with this process, we employed a comparative proteomics approach using isobaric, stable isotope coded labels to compare the proteomes of potato tubers after 0 and 5 months of storage at 5 degrees C. We evaluated both high pH reverse phase (hpRP) liquid chromatography (LC) and off-gel electrophoresis (OGE) as first dimension fractionation methods followed by nanoLC-MS/MS using two high performance mass spectrometry platforms (Q-TOF and Orbitrap). We found that hpRP LC consistently offered better resolution and a more MS-compatible workflow than OGE and it consistently yielded more unique peptide/protein identifications and high sequence coverage with better quantification. In this study, a total of 4,463 potato proteins were identified and 46 proteins showed differential expression during potato tubers cold storage. Several key proteins important in controlling starch-sugar conversion that leads to cold-induced sweetening, as well as other proteins that are potentially involved in this process were successfully identified. Our results suggest that the hpRP-RP shotgun approach is feasible and a practical workflow for discovering potential protein candidates in plant global proteomic analysis.