PXD010710

PXD010710 is an original dataset announced via ProteomeXchange.

Title	Comprehensive evaluation of RNAlater effect on proteome and phosphoproteome
Description	Tumors such as pancreatic cancer contain a variety of enzymes including DNases, RNases and proteases which may lead to autolysis of DNA, RNA and proteins during sample processing. In general, RNAlater can be used to keep nucleic acids intact since it contains high concentrations of quaternary ammonium sulfates which denature those enzymes. Although a few studies were carried out to find effect of RNAlater mainly on DNA and RNA, it is largely unknown whether RNAlater affect both proteome and phosphoproteome. Thus, we carried out a systematic and comprehensive analysis of the RNAlater effect on the proteome and phosphoproteome using high-resolution mass spectrometry. Pancreatic tumor tissues from three patients were pulverized using Covaris CP02 Cryoprep device and incubated in RNAlater at 4 °C for 24 hours. We used the 6-plex TMT to measure quantitative information of proteome and phosphoproteome. Peptides fractionated by mid pH reverse phase liquid chromatography were divided into two parts: a portion (~8%) of each mRP fraction was used to profile the global proteome and the rest (~92%) was to survey phosphorylation enriched by IMAC–based approach. As a result, the global profiling identified 186,941 unmodified peptides of 9,152 protein groups, 18,705 phosphopeptides (15,842 phosphosites). When analyzing the unbiased proteomics and phosphoproteomics data, we observed no significant quantitative changes in both proteins and phosphorylation, if any, induced by RNAlater. Therefore, this result confirms that stored tissues in RNAlater do not significantly affect the proteome and phosphoproteome of pancreatic cancer tumors.
HostingRepository	PRIDE
AnnounceDate	2019-05-06
AnnouncementXML	Submission_2019-05-06_10:51:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Min-Sik Kim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-07 03:52:05	ID requested
⏵ 1	2019-05-06 10:51:34	announced

Bae J, Kim SJ, Lee SE, Kwon W, Kim H, Han Y, Jang JY, Kim MS, Lee SW, Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation. Clin Proteomics, 16():18(2019) [pubmed]

ProteomeXchange project tag: Cancer (B/D-HPP)

curator keyword: Biological

submitter keyword: RNAlater, proteome,phosphoproteome

Min-Sik Kim
contact affiliation	Department of Applied Chemistry, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, South Korea
contact email	ms_kim@khu.ac.kr
lab head
Min-Sik Kim
contact affiliation	Kyung Hee University, Applied Chemistry
contact email	ms2scan@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/05/PXD010710

PRIDE project URI

• PRIDE
  1. PXD010710
     1. Label: PRIDE project
     2. Name: Comprehensive evaluation of RNAlater effect on proteome and phosphoproteome