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Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation

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dc.contributor.authorBae, Jingi-
dc.contributor.authorKim, Su-Jin-
dc.contributor.authorLee, Seung-Eun-
dc.contributor.authorKwon, Wooil-
dc.contributor.authorKim, Hongbeom-
dc.contributor.authorHan, Youngmin-
dc.contributor.authorJang, Jin-Young-
dc.contributor.authorKim, Min-Sik-
dc.contributor.authorLee, Sang-Won-
dc.date.accessioned2019-05-13T04:47:36Z-
dc.date.available2019-05-13T13:48:36Z-
dc.date.issued2019-04-25-
dc.identifier.citationClinical Proteomics,16(1):18ko_KR
dc.identifier.issn1559-0275-
dc.identifier.urihttp://hdl.handle.net/10371/153250-
dc.description.abstractCertain tumors such as pancreatic ductal adenocarcinoma (PDAC) are known to contain a variety of hydrolytic enzymes including RNases and proteases that may lead to degradation of RNA and proteins during sample processing. For such tumor tissues with RNA instability, RNAlater containing a high concentration of quaternary ammonium sulfates that denature RNA-hydrolyzing enzymes is often used to protect RNAs from hydrolysis. Although a few studies have been carried out to determine the effect of RNAlater on DNA and RNA, whether RNAlater influences the proteome and phosphoproteome is largely unknown. In this study we carried out a systematic and comprehensive analysis of the effect of RNAlater on the proteome and phosphoproteome using high-resolution mass spectrometry. PDAC tissues from three patients were individually pulverized and the tissue powders of each patient were divided into two portions, one of which was incubated in RNAlater at 4 °C for 24 h (RNAlater tissue) while the other was kept at – 80 °C (frozen tissue). Comprehensive quantitative profiling experiments on the RNAlater tissues and the frozen tissues resulted in the identification of 99,136 distinct peptides of 8803 protein groups and 17,345 phosphopeptides of 16,436 phosphosites. The data exhibited no significant quantitative changes in both proteins and phosphorylation between the RNAlater tissues and the frozen tissue. In addition, the phosphoproteome data showed heterogeneously activated pathways among the three patients that were not altered by RNAlater. These results indicate that the tissue preservation method using RNAlater can be effectively used on PDAC tissues for proteogenomic studies where preservation of intact DNA, RNA and proteins is prerequisite. Data from this study are available via ProteomeXchange with the identifier PXD010710.ko_KR
dc.description.sponsorshipNational Research Foundation funded by the Ministry of Science and ICT (Grant Nos. NRF-2017M3C7A1027472, NRF-2017M3C9A5031397, 2019R1C1C1006262).ko_KR
dc.language.isoenko_KR
dc.publisherBioMed Centralko_KR
dc.titleComprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylationko_KR
dc.typeArticleko_KR
dc.contributor.AlternativeAuthor배진기-
dc.contributor.AlternativeAuthor김수진-
dc.contributor.AlternativeAuthor이승은-
dc.contributor.AlternativeAuthor권우일-
dc.contributor.AlternativeAuthor김홍범-
dc.contributor.AlternativeAuthor한영민-
dc.contributor.AlternativeAuthor장진영-
dc.contributor.AlternativeAuthor김민식-
dc.contributor.AlternativeAuthor이상원-
dc.identifier.doi10.1186/s12014-019-9239-z-
dc.language.rfc3066en-
dc.rights.holderThe Author(s)-
dc.date.updated2019-04-28T03:36:37Z-
Appears in Collections:
College of Medicine/School of Medicine (의과대학/대학원)Surgery (외과학전공)Journal Papers (저널논문_외과학전공)
College of Medicine/School of Medicine (의과대학/대학원)Cancer Research Institute (암연구소)Journal Papers (저널논문_암연구소)
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