PXD014240

PXD014240 is an original dataset announced via ProteomeXchange.

Title	Combination of proteogenomics with peptide de novo sequencing identifies new genes and hidden posttranscriptional modifications
Description	Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in detection of 104 hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single amino acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Co-expression and phylostratigraphic analysis of the refined proteome suggests new functions in evolutionary young genes correlated with distinct developmental stages. In conclusion, our advanced proteogenomics approach is highly supportive to promote functional studies of model systems. Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in detection of 104 hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single amino acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Co-expression and phylostratigraphic analysis of the refined proteome suggests new functions in evolutionary young genes correlated with distinct developmental stages. In conclusion, our advanced proteogenomics approach is highly supportive to promote functional studies of model systems.
HostingRepository	PRIDE
AnnounceDate	2019-09-25
AnnouncementXML	Submission_2019-10-25_05:59:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bernhard Blank-Landeshammer
SpeciesList	scientific name: Sordaria macrospora; NCBI TaxID: 5147;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-13 00:23:49	ID requested
1	2019-09-25 05:27:35	announced
⏵ 2	2019-10-25 05:59:19	announced	2019-10-25: Updated publication reference for PubMed record(s): 31615963.

Blank-Landeshammer B, Teichert I, M, ä, rker R, Nowrousian M, K, ü, ck U, Sickmann A, Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications. mBio, 10(5):(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Sordaria macrospora, LC-MSMS, de novo peptide sequencing, Proteogenomics, RNA Editing

Albert Sickmann
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
contact email	sickmann@isas.de
lab head
Bernhard Blank-Landeshammer
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund
contact email	bernhard.blank@isas.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014240
     1. Label: PRIDE project
     2. Name: Combination of proteogenomics with peptide de novo sequencing identifies new genes and hidden posttranscriptional modifications