prot.raw: proteinGroups file from MaxQuant of a TMT experiment of...
In demar01/protrusionproteome: protrusionproteome

Description Usage Format Value Source

The dataset contains the proteinGroup.txt output file for protrusions and bodies deposited in PRIDE identifier PXD021239, generated by Dermit et al 2020. The dataset contains the proteingroups output file from MaxQuant.

prot.raw

A dataframe with 5905 rows and 107 variables:

Protein.IDs: Uniprot IDs
Majority.protein.IDs: Uniprot IDs of major protein(s) in the protein group
Razor...unique.peptides: Number of peptides used for the quantification of this protein group
Unique.peptides: Number of peptides identified which are unique for this protein group
Reporter.intensity.corrected. (10): TMT-MS3 quantitative relative abundance metrics.Reporter intensity correct x where x ranges from 0 to 9. Reporter intensity correct 0 corresponds to the TMT 126C TMT tag, Reporter intensity correct 1 corresponds to the TMT 127N TMT tag, and so on. Reporter intensity correct 9 corresponds to the TMT 131N tag
Protein.names: Full protein names
Gene.names: Gene name
Fasta.headers: Header as present in the Uniprot fasta file
Only.identified.by.site: The protein is only identified by a modification site if marked ('+')
Reverse: The protein is identified in the decoy database if marked ('+')
Potential.contaminant: The protein is a known contaminant if marked ('+')

A data.frame.

Dermit et al 2020. Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells. Developmental Cell Volume 55, Issue 3, 9 November 2020, Pages 298-313.e10. doi.org/10.1016/j.devcel.2020.10.006.

demar01/protrusionproteome documentation built on April 29, 2021, 5:47 a.m.