GFPip: GFPip - EED protein interactors (IP-MS dataset)
In arnesmits/DEPstoi: Stoichiometry analysis of label-free proteomics data

The GFPip dataset contains label free quantification (LFQ) and intensity-based absolute quantification (iBAQ) data for EED protein interactors in embryonic stem cells, generated by Kloet et al 2016. The dataset contains the proteingroups output file from MaxQuant.

GFPip

A data.frame with 1914 observations and 30 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 (6): Raw mass spectrometry intensity, A.U.
iBAQ columns (6): iBAQ normalized mass spectrometry intensity, A.U.
LFQ.intensity columns (6): 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 ('+')
Contaminant: The protein is a known contaminant if marked ('+')
id: The protein group ID

A data.frame with the GFPip dataset

Kloet et al (2016). The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation. Nature Structural & Molecular Biology 23(7): 682-90. doi: 10.1038/nsmb.3248

arnesmits/DEPstoi documentation built on May 3, 2019, 4:31 p.m.