PXD034107

PXD034107 is an original dataset announced via ProteomeXchange.

Title	Nematode gene annotation by machine learning assisted proteotranscriptomics enables proteome-wide evolutionary analysis
Description	Nematodes encompass over 24,000 described species, which were discovered in almost every ecological habitat, and make up over 80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to around 650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine learning quality control in an approach called proteotranscriptomics, we improve gene annotations for 9 genome-sequenced nematode species and provide new gene annotations for 3 additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans. Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.
HostingRepository	PRIDE
AnnounceDate	2022-11-12
AnnouncementXML	Submission_2022-11-12_11:05:48.213.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	FButter
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-25 03:20:53	ID requested
⏵ 1	2022-11-12 11:05:48	announced

Dataset with its publication pending

submitter keyword: LC-MS/MS

proteotranscriptomics

FalkButter
contact affiliation	Institute of Molecular Biology (IMB)
contact email	f.butter@imb.de
lab head
FButter
contact affiliation	Quantitative Proteomics Institute of Molecular Biology (IMB)
contact email	f.butter@imb-mainz.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/2022/11/PXD034107

PRIDE project URI

• PRIDE
  1. PXD034107
     1. Label: PRIDE project
     2. Name: Nematode gene annotation by machine learning assisted proteotranscriptomics enables proteome-wide evolutionary analysis