PXD005423

PXD005423 is an original dataset announced via ProteomeXchange.

Title	Proteome of the Apogamous Fern Dryopteris affinis ssp. affinis
Description	Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a “species-specific transcriptome database” (SSTDB). In total 1397 protein clusters with 5865 unique peptide sequences were identified (13 decoy proteins out of 1410, protFDR 0.93% on protein cluster level). We show that using a “species-specific transcriptome database” for protein identification increases the number of identified peptides almost four times compared to using only the publically available viridiplantae database. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:34:38.974.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonas Grossmann
SpeciesList	scientific name: Dryopteris affinis subsp. affinis; NCBI TaxID: 239549;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-22 07:25:59	ID requested
1	2017-04-11 06:50:36	announced
⏵ 2	2024-10-22 04:34:42	announced	2024-10-22: Updated project metadata.

10.3389/fpls.2017.00336;

Grossmann J, Fern, á, ndez H, Chaubey PM, Vald, é, s AE, Gagliardini V, Ca, ñ, al MJ, Russo G, Grossniklaus U, . Front Plant Sci, 8():336(2017) [pubmed]

ProteomeXchange project tag: PRIME-XS Project

curator keyword: Biological

submitter keyword: plant proteomics,Orbitrap LC-MSMS, species-specific transcriptome database, RNA-seq database, fern, Dryopteris affinis ssp. affinis

ELENA MARIA FERNANDEZ GONZALEZ
contact affiliation	Universidad de Oviedo Area of Plant Physiology, Dept. BOS Catedrático R Uria s/n 33071 Oviedo Spain.
contact email	fernandezelena@uniovi.es
lab head
Jonas Grossmann
contact affiliation	Functional Genomics Center Zurich (UZH/ETHZ)
contact email	jg@fgcz.ethz.ch
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/2017/04/PXD005423

PRIDE project URI

• PRIDE
  1. PXD005423
     1. Label: PRIDE project
     2. Name: Proteome of the Apogamous Fern Dryopteris affinis ssp. affinis