Dataset Information

Proteogenomics Pipeline For Pineapple

ABSTRACT: Here we have undertaken a pilot study analysing the proteome of MD2 pineapple using Liquid Chromatography coupled with Mass Spectrometry (LC-MS/MS) and identified 3,818 peptides from 1,781 candidate proteins in the annotated V3 genome sequenced. In addition, a further 603 peptide identifications were found that mapped exclusively to an independent MD2 transcriptome-derived database and were not found in the standard V3 annotated proteome. Peptide identifications derived from the MD2 transcripts were also cross-referenced to a more recent and complete MD2 genome annotation, resulting in 402 non overlapping peptides with either of the genomes. Subsequently, cross-referencing these peptide identifications via their parent transcripts, 30 high-quality gene candidates novel to the V3 pineapple genomes were identified. These analyses add to the knowledge of experimentally validated pineapple genes and demonstrate the utility of transcript-derived proteomics to discover both novel genes and genetic structure in plant genome, and can help improve its annotation.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Ananas Comosus

TISSUE(S): Leaf

SUBMITTER: David Newman

LAB HEAD: Simon Hubbard

PROVIDER: PXD045998 | Pride | 2024-05-24

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20170418_SH_NA_120min_prec_01.mzML	Mzml
	20170418_SH_NA_120min_prec_01.raw	Raw
	20170418_SH_NA_120min_prec_02.mzML	Mzml
	20170418_SH_NA_120min_prec_02.raw	Raw
	20170418_SH_NA_120min_prec_03.mzML	Mzml

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Publications

Proteogenomic Gene Structure Validation in the Pineapple Genome.

Ariffin Norazrin N Newman David Wells DW Nelson Michael G MG O'cualain Ronan R Hubbard Simon J SJ

Journal of proteome research 20240423 5

MD2 pineapple (<i>Ananas comosus</i>) is the second most important tropical crop that preserves crassulacean acid metabolism (CAM), which has high water-use efficiency and is fast becoming the most consumed fresh fruit worldwide. Despite the significance of environmental efficiency and popularity, until very recently, its genome sequence has not been determined and a high-quality annotated proteome has not been available. Here, we have undertaken a pilot proteogenomic study, analyzing the proteo ...[more]

PMID: 38651221

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