UbiLength: UbiLength - Ubiquitin interactors of different linear...
In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

Description Usage Format Value Source

The UbiLength dataset contains label free quantification (LFQ) data for ubiquitin interactors of different linear ubiquitin lengths, generated by Zhang et al 2017. The dataset contains the proteingroups output file from MaxQuant.

UbiLength

A data.frame with 3006 observations and 35 variables:

Protein.IDs: Uniprot IDs
Majority.protein.IDs: Uniprot IDs of major protein(s) in the protein group
Protein.names: Full protein names
Gene.names: Gene name
Fasta.headers: Header as present in the Uniprot fasta file
Peptides: Number of peptides identified for this 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
Intensity columns (12): Raw mass spectrometry intensity, A.U.
LFQ.intensity columns (12): LFQ normalized mass spectrometry intensity, A.U.
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.

Zhang, Smits, van Tilburg, et al (2017). An interaction landscape of ubiquitin signaling. Molecular Cell 65(5): 941-955. doi: 10.1016/j.molcel.2017.01.004.

arnesmits/DEP documentation built on Aug. 7, 2019, 10:44 a.m.