PXD005643

PXD005643 is an original dataset announced via ProteomeXchange.

Title	Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides
Description	Computational, genomic, and proteomic approaches have been used to discover nonannotated proteincoding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:35:14.877.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiao Ma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-01-03 02:41:30	ID requested
1	2017-10-17 01:12:42	announced
⏵ 2	2024-10-22 04:35:17	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.6b00191;

Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A, Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Anal Chem, 88(7):3967-75(2016) [pubmed]

curator keyword: Technical

submitter keyword: smORF-encoded polypeptides (SEPs), LC-MS

Alan Saghatelian
contact affiliation	Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
contact email	asaghatelian@salk.edu
lab head
Jiao Ma
contact affiliation	Salk Institute
contact email	jma@salk.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/2017/10/PXD005643

PRIDE project URI

• PRIDE
  1. PXD005643
     1. Label: PRIDE project
     2. Name: Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides