PXD012999-3

PXD012999 is an original dataset announced via ProteomeXchange.

Title	Proteomics and proteogenomics analysis of sweet potato (Ipomoea batatas) leaf and root
Description	Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweet potato. A total of 74,255 peptides corresponding to 4,321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomea species and mapped on the sweet potato transcriptome and haplotype-resolved genome. A proteogenomics analysis successfully mapped 12,902 peptides against the transcriptome or genome, representing 90.4% of the total 14,275 uniquely identified peptides, predicted 741 new protein-coding genes, and specified 2726 loci where annotations can be further improved. Overall, 39,916 peptides mapped to 3,143 unique proteins in leaves, and 34,339 peptides mapped to 2,928 unique proteins in roots; 32% and 27% unique identified proteins were leaves- and roots-specific, respectively.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:55:31.693.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	George Popescu
SpeciesList	scientific name: Ipomoea batatas; NCBI TaxID: 4120;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-06 07:12:38	ID requested
1	2019-05-29 19:04:19	announced
2	2021-02-15 22:54:33	announced	2021-02-16: Updated project metadata.
⏵ 3	2024-10-22 04:55:32	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: proteogenomics,Sweet potato, storage root proteome, leaf proteome, LC-MS/MS

George V Popescu
contact affiliation	Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39759, USA
contact email	gvp18@msstate.edu
lab head
George Popescu
contact affiliation	IGBB, Mississippi State University
contact email	gvp18@msstate.edu
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/PXD012999

PRIDE project URI

• PRIDE
  1. PXD012999
     1. Label: PRIDE project
     2. Name: Proteomics and proteogenomics analysis of sweet potato (Ipomoea batatas) leaf and root