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Cooper Salvia columbariae chia seeds, roots, hypocotyls, and cotyledons

ABSTRACT: Cooper sought to increase the sensitivity of peptide detection and broaden the range of tissues covered through his analysis of chia proteomes. Targeted tissues were ungerminated seeds and the roots, hypocotyls, and cotyledons of five-day-old seedlings. As in Husselmann 2017, TCEP was employed for reducing disulfides, but iodoacetamide alkylated the cysteines. Mass spectrometry took place at the Mass Spectrometry and Proteomics Facility at the Johns Hopkins School of Medicine. The Thermo Orbitrap Fusion Lumos Tribrid mass spectrometer yielded an average of 54,868 tandem mass spectra per LC-MS/MS experiment, producing up to twenty MS/MS per second at its peak.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Salvia Columbariae (ncbitaxon:95165)

SUBMITTER: Bret Cooper

PROVIDER: MSV000086863 | MassIVE | Mon Feb 15 04:04:00 GMT 2021

SECONDARY ACCESSION(S): PXD024181

REPOSITORIES: MassIVE

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Publications

Proteomic Identification and Meta-Analysis in <i>Salvia hispanica</i> RNA-Seq de novo Assemblies.

Klein Ashwil A Husselmann Lizex H H LHH Williams Achmat A Bell Liam L Cooper Bret B Ragar Brent B Tabb David L DL

Plants (Basel, Switzerland) 20210414 4

While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcri ...[more]

PMID: 33919777

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