PXD000317

PXD000317 is an original dataset announced via ProteomeXchange.

Title	Rice embryogenesis proteins quantification (Zi)
Description	We've conducted iTRAQ based quantitative proteomics on rice embryogenesis and discover hundreds of proteins whose abundances could be regulated acively. To further validate the protein abundances change profiles, we conducted MRM experiment to do validation. growth: Five embryogenesis stages (6, 12, 18, 24 and 30 days after pollination)rice embryos were collected first. Then proteins of these stages were extracted by using 8 M urea lysis. Two microgram proteins digests of each stages were injected to ABSciex QTRAP 5500 three times for MRM screen. treatment: Normal rice strain 9711 were grown in the rice field in Hunan Hybrid Rice Research and Developmental center. No special treatment were conducted to the rice strain. extraction: Rice embryos were ground to a fine powder and were suspended in lysis buffer containing 8 M Urea, 10 mM DTT, 1 mM phenylmethyl sulfonyl fluoride, 2 mM EDTA, and 20 mM Tris-HCl, pH 8.5. After centrifugation at 20 000 g for 30 min, the protein concentrations of the supernatant were determined using the Bradford assay. separation: Total protein digests were loaded onto the C 18 column (separated over a 40 min acetonitrile gradient from 5 to 35% in 0.1% FA ) and no pre-separation techniques were conducted. digestion: Twenty microgram protein solutions from each embryogenesis stage were diluted 4 times with 25 mM NH4CO3, digested with 1 ul trypsin (0.5 ug/ul) and incubated at 37 C overnight. Digestion was stopped by adding TFA to a concentration of 0.1%. acquisition: MRM mode was used to survey the samples. informatics: For MRM confirmation, the raw data of MRM was processed by using MultiQuant 2.0.2 (AB SCIEX, Framingham, MA, USA). After manual inspection and retention alignment, peaks with an S/N>10 were qualified for quantification. To calculate the protein abundance of a protein in a specific embryogenesis stages, we use the sum of all the transition areas of a protein as an indicator of the protein abundance. And the average sum areas of three technical replicates indicate the final protein abundances of a stage. Finally, the abundances and ratios of each stage to 6 DAP were calculated by perl programming script. The comparisons and scatter plots of the MRM and iTRAQ/Shotgun quantitative data were assembled using Excel (Microsoft Office 2010, the USA).
HostingRepository	PeptideAtlas
AnnounceDate	2014-10-21
AnnouncementXML	Submission_2014-10-21_11:03:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jin Zi
SpeciesList	scientific name: Oryza sativa; NCBI TaxID: 39947;
ModificationList	S-carboxamidomethyl-L-cysteine
Instrument	QTRAP 5500

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-02 14:11:39	ID requested
1	2013-07-02 15:19:30	announced
2	2014-03-12 13:28:27	announced	update LabHead
⏵ 3	2014-10-21 11:03:35	announced	update reference

Zi J, Zhang J, Wang Q, Zhou B, Zhong J, Zhang C, Qiu X, Wen B, Zhang S, Fu X, Lin L, Liu S, Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One, 8(9):e74229(2013) [pubmed]

curator keyword: selected reaction monitoring, SRM, targeted

Jin Zi
contact affiliation	Chinese Academy of Sciences
contact email	zij@genomics.cn
dataset submitter
Siqi Liu
contact affiliation	Chinese Academy of Sciences
contact email	siqiliu@genomics.cn
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI