PXD010153-1

PXD010153 is an original dataset announced via ProteomeXchange.

Title	Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues
Description	Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA ratios (PTR) and a quantification of their effects is still lacking. Here we quantified PTRs for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We analyzed the contribution of known sequence determinants of protein synthesis and degradation and 13 novel mRNA and protein sequence motifs that we found by association testing. While the dynamic range of PTR spans more than 2 orders of magnitude, our integrative model predicts PTR at a median precision of 3.2-fold. A reporter assay provided significant functional support for two novel UTR motifs and a proteome-wide competition-binding assay identified motif-specific bound proteins for one of them. Moreover, our direct comparison of protein to RNA level leads to a new metrics of codon optimality. Altogether, this study shows that a large fraction of PTR variance across genes can be predicted from sequence and identify many new candidate post-transcriptional regulatory elements in the human genome.
HostingRepository	PRIDE
AnnounceDate	2018-07-02
AnnouncementXML	Submission_2018-07-02_01:32:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dongxue Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	L-methionine sulfoxide; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-18 06:12:24	ID requested
⏵ 1	2018-07-02 01:32:17	announced
2	2019-02-22 00:34:52	announced	Updated project metadata.
3	2024-10-22 04:50:42	announced	2024-10-22: Updated project metadata.

10.1101/357137;

curator keyword: Biological

submitter keyword: RNA pulldown

Bernhard Küster
contact affiliation	Chair of Proteomics and Bioanalytics, Technische Universität München, Germany
contact email	kuster@tum.de
lab head
Dongxue Wang
contact affiliation	Chair of Proteomics and Bioanalytics, Technical University of Munich
contact email	dx.wang@tum.de
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/2018/07/PXD010153

PRIDE project URI

• PRIDE
  1. PXD010153
     1. Label: PRIDE project
     2. Name: Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues