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DDA annotation of MSMS spectra for a threespine stickleback liver proteome spectral library

ABSTRACT: DDA data searched against G. aculeatus reference proteome to annotate PSMs with peptide sequence, precursor and fragment ion, protein AC, m/z, z, and RT information for spectral library construction. All data are from G. aculeatus liver tissue. Livers were collected from fish acclimated to either 7, 15, or 25C. Fish were from two populations in California (Klamath River and Big Lagoon). Experiments were performed by Bryn Levitan in the Kültz Laboratory at UC Davis.

INSTRUMENT(S): impact II

ORGANISM(S): Gasterosteus Aculeatus (ncbitaxon:69293)

SUBMITTER: Dietmar Kueltz

PROVIDER: MSV000087672 | MassIVE | Mon Jun 21 00:53:00 BST 2021

SECONDARY ACCESSION(S): PXD026823

REPOSITORIES: MassIVE

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Project description:This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs) affecting host resistance responses. In order to identify an appropriate RIL population to map QTL controlling disease resistance responses, we performed a parental survey of 7 different Arabidopsis accessions. We treated vegetatively grown plants with either salicylic acid or a control solution, and harvested the plants at 3 different time points after chemical treatment. We present Affymetrix GeneChip microarray expression data for 3 biological replications of this parental survey. Experimenter name = Dina St. Clair; Experimenter phone = (530) 752-1740; Experimenter department = Department of Plant Sciences; Experimenter institute = UC Davis; Experimenter address = UC Davis Campus; Experimenter address = 114 Amundson Hall; Experimenter address = Davis, California; Experimenter zip/postal_code = CA; Experimenter country = USA Experiment Overall Design: 18 samples were used in this experiment

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DDA annotation of MSMS spectra for a threespine stickleback liver proteome spectral library

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