MassIVE MSV000079780

Partial Public PXD004239

Agave Americana Diel Proteome

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Description

Agave americana 3 year-old clones were allowed to grow for one month under greenhouse 12h/12h light/dark conditions with regular irrigation. Three biological replicates of mature leaf were flash-frozen and ground under liquid nitrogen. Each cell pellet was resuspended in SDS buffer and sonicated. Proteins were extracted via TCA precipitation. Samples were denatured and reduced followed by enzymatic digestion using trypsin. Samples were analyzed via 2D (SCX-RP) nano-LC-MS/MS on an Orbitrap-Velos-Pro. MS/MS spectra were searched and filtered with MyriMatch and IDPicker. Note, the Peak List and Result files do not have the same sample description as found in the published manuscript. Please use the key provided in the Supplemental Files. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: CAM, proteomics, Agave, diel cycle

Contact

Principal Investigators:
(in alphabetical order) 		Xiaohan Yang
Submitting User: pabraham
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Experimental Design
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Identification Results
    Proteins (Human, Remapped):
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    Variant Peptides:
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Quantification Results
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.