PXD008586

PXD008586 is an original dataset announced via ProteomeXchange.

Title	Small Protein Enrichment-Based Proteogenomics Identifies Plentiful Missing Proteins and Three Novel sORFs in Saccharomyces cerevisiae
Description	Small proteins (SPs) are defined as peptides of 100 amino acids or less encoded by short open reading frames (sORFs). Recent studies have shown that SPs are involved in many important biological processes, including cell signaling, metabolism, growth and so on. However, most of the annotated SPs in almost all species are currently lacking the evidence for protein existence and are regard as missing proteins (MPs). In addition, more and more mis-annotated sORFs have been discovered by proteogenomic methods in human, mice and even the well-characterised Saccharomyces cerevisiae. This reveals a blind spot in traditional gene annotation technology for those SPs-encoding genes. Because SPs are short and generally low abundant, SPs identification using proteomics faces challenges. A deeper coverage of SPs identification may help validate more MPs and discover more potential mis-annotated sORFs. Here, we applied a SPs enrichment-based proteogenomic strategy to Saccharomyces cerevisiae. By integrating four different SPs enrichment methods, we have successfully validated 31 MPs and discovered 3 novel sORFs (YKL104W-A, YHR052C-B and YHR054C-B) which were verified by novel peptide synthesis. In-depth analysis of our SPs enrichment datasets also reveals a series of special physicochemical and biological characteristics of SPs and particular rules of SPs identification. Based on these, we then systematically conclude the difficulties, causes and solutions in SPs identification.
HostingRepository	PRIDE
AnnounceDate	2018-06-15
AnnouncementXML	Submission_2018-06-15_03:52:19.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	cuitong he
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-03 01:31:11	ID requested
1	2018-06-15 03:31:24	announced
⏵ 2	2018-06-15 03:52:20	announced	Updated project metadata.

Dataset with its publication pending

curator keyword: Technical, Biological

submitter keyword: yeast, proteogenomics, small proteins, short open reading frames, missing proteins, enrichment

Ping Xu
contact affiliation	Beijing Proteome Research Center, 38 Science Park Road, Changping District, Beijing 102206, China.
contact email	xuping@mail.ncpsb.org
lab head
cuitong he
contact affiliation	National Center for Protein Sciences·Beijing
contact email	hecuitongpro@163.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008586
     1. Label: PRIDE project
     2. Name: Small Protein Enrichment-Based Proteogenomics Identifies Plentiful Missing Proteins and Three Novel sORFs in Saccharomyces cerevisiae