PXD004010-1

PXD004010 is an original dataset announced via ProteomeXchange.

Title	JUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells
Description	Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMPg creates multiple databases of DNA polymorphisms, mutations, splice junctions, partially trypticity, as well as protein fragments translated from the whole transcriptome in all six frames after RNA-seq de novo assembly. We use a multistage strategy to search these databases sequentially, in which the performance is optimized by re-searching only unmatched high quality spectra, and re-using amino acid tags generated by the JUMP search engine. The identified peptides/proteins are displayed with gene loci using the UCSC genome browser. The JUMPg is applied to process a label-free mass spectrometry dataset of Alzheimer’s disease postmortem brain, uncovering 496 new peptides of amino acid substitutions, alternative splicing, frame shift, and “non-coding gene” translation. The novel protein PNMA6BL specifically expressed in the brain is highlighted. We also tested JUMPg to analyze a stable-isotope labeled dataset of multiple myeloma cells, revealing 991 sample-specific peptides that include protein sequences in the immunoglobulin light chain variable region. Thus, the JUMPg program is an effective proteogenomics tool for multi-omics data integration.
HostingRepository	PRIDE
AnnounceDate	2017-02-20
AnnouncementXML	Submission_2017-02-20_07:33:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	xusheng wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-19 03:10:17	ID requested
⏵ 1	2017-02-20 07:33:03	announced

Li Y, Wang X, Cho JH, Shaw TI, Wu Z, Bai B, Wang H, Zhou S, Beach TG, Wu G, Zhang J, Peng J, JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. J Proteome Res, 15(7):2309-20(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Genomics, proteomics, mass spectrometry, proteogenomics, RNA-seq, database search, multistage analysis, spectrum quality control

Junmin Peng
contact affiliation	St. Jude Children's Research Hospital
contact email	junmin.peng@stjude.org
lab head
xusheng wang
contact affiliation	Proteomics
contact email	xushengwang78@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/2017/02/PXD004010

PRIDE project URI

• PRIDE
  1. PXD004010
     1. Label: PRIDE project
     2. Name: JUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells