PXD010618

PXD010618 is an original dataset announced via ProteomeXchange.

Title	Peptimapper - Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes
Description	Background: Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. Results: Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus siliculosus, a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. Conclusions: Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:47:14.643.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	cloarec laetitia
SpeciesList	scientific name: Ectocarpus siliculosus (Brown alga); NCBI TaxID: 2880;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-30 06:00:36	ID requested
1	2019-01-22 06:19:31	announced
⏵ 2	2024-10-22 04:47:15	announced	2024-10-22: Updated project metadata.

10.1186/s12864-019-5431-9;

Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C, Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics, 20(1):56(2019) [pubmed]

curator keyword: Technical

submitter keyword: genome annotation, peptide sequence tag, proteogenomics, proteomics, tandem mass spectrometry,bioinformatics

Laetitia Guillot
contact affiliation	Protim, Univ Rennes, Inserm, EHESP, Irset – UMR_S 1085
contact email	laetitia.guillot@univ-rennes1.fr
lab head
cloarec laetitia
contact affiliation	université de rennes
contact email	laetitia.guillot@univ-rennes1.fr
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/2019/01/PXD010618

PRIDE project URI

• PRIDE
  1. PXD010618
     1. Label: PRIDE project
     2. Name: Peptimapper - Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes