PXD007166

PXD007166 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	nextPP for chromosome-based proteomic research using neXtProt and GENCODE databases
Description	In this study, we introduce a streamlined pipeline using customized and concatenated GENCODE and neXtProt databases with controlled false discovery rate (FDR) for finding GENCODE ASVs and missing proteins while mapping onto single amino acid variants (SAAVs) from Hippocampal dataset.
HostingRepository	MassIVE
AnnounceDate	2017-11-03
AnnouncementXML	Submission_2017-11-03_05:37:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Heeyoun Hwang
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	iodoacetamide - site C
Instrument	LTQ Orbitrap; LTQ Orbitrap Elite; Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-01 09:02:07	ID requested
⏵ 1	2017-11-03 05:37:45	announced

Publication List

Hwang H, Park GW, Park JY, Lee HK, Lee JY, Jeong JE, Park SR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases. J Proteome Res, 16(12):4425-4434(2017) [pubmed]
Hwang H, Park GW, Kim KH, Lee JY, Lee HK, Ji ES, Park SK, Xu T, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases. J Proteome Res, 14(12):5028-37(2015) [pubmed]
Kwon KH, Kim JY, Kim SY, Min HK, Lee HJ, Ji IJ, Kang T, Park GW, An HJ, Lee B, Ravid R, Ferrer I, Chung CK, Paik YK, Hancock WS, Park YM, Yoo JS, Chromosome 11-centric human proteome analysis of human brain hippocampus tissue. J Proteome Res, 12(1):97-105(2013) [pubmed]
Park GW, Hwang H, Kim KH, Lee JY, Lee HK, Park JY, Ji ES, Park SR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate. J Proteome Res, 15(11):4082-4090(2016) [pubmed]

Hwang H, Park GW, Park JY, Lee HK, Lee JY, Jeong JE, Park SR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases. J Proteome Res, 16(12):4425-4434(2017) [pubmed]

Hwang H, Park GW, Kim KH, Lee JY, Lee HK, Ji ES, Park SK, Xu T, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases. J Proteome Res, 14(12):5028-37(2015) [pubmed]

Kwon KH, Kim JY, Kim SY, Min HK, Lee HJ, Ji IJ, Kang T, Park GW, An HJ, Lee B, Ravid R, Ferrer I, Chung CK, Paik YK, Hancock WS, Park YM, Yoo JS, Chromosome 11-centric human proteome analysis of human brain hippocampus tissue. J Proteome Res, 12(1):97-105(2013) [pubmed]

Park GW, Hwang H, Kim KH, Lee JY, Lee HK, Park JY, Ji ES, Park SR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate. J Proteome Res, 15(11):4082-4090(2016) [pubmed]

Keyword List

submitter keyword: C-HPP, alternative splicing variant, single amino acid variant

submitter keyword: C-HPP, alternative splicing variant, single amino acid variant

Contact List

Jong Shin Yoo
contact affiliation	Korea Basic Science Institute
contact email	jongshin@kbsi.re.kr
lab head
Heeyoun Hwang
contact affiliation	KBSI
contact email	heeyounh@kbsi.re.kr
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/MSV000081385

MassIVE dataset URI

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://massive.ucsd.edu/MSV000081385