data.frame with PSM-level quantitation data by Christoforou et al.
(2016). This is the first replicate of a spatial proteomics dataset from a
hyperLOPIT experimental design on Mouse E14TG2a embryonic stem
cells. Normalised intensities for proteins for TMT 10-plex labelled
fractions are available for 3 replicates acquired in MS3 mode using an
Orbitrap Fusion mass-spectrometer.
The variable names are
X126, X127C, X127N, X128C, X128N, X129C, X129N, X130C, X130N and X131: the 10 TMT tags used to quantify the peptides along the density gradient.
Sequence: the peptide sequence.
ProteinDescriptions: the description of the protein this peptide was associated to.
NbProteins: the number of proteins in the protein group.
ProteinGroupAccessions: the main protein accession number in the protein group.
Modifications: post-translational modifications identified in the peptide.
qValue: the PSM identification q-value.
PEP: the PSM posterior error probability.
IonScore: the Mascot ion identification score.
NbMissedCleavages: the number of missed cleavages in the peptide.
IsolationInterference: the calculated precursor ion isolation interference.
IonInjectTimems: the ions injection time in milli-seconds.
Intensity: the precursor ion intensity.
Charge: the peptide charge.
mzDa: the peptide mass to charge ratio, in Daltons.
MHDa: the peptide mass, in Daltons.
DeltaMassPPM: the difference in measure and calculated mass, in parts per millions.
RTmin: the peptide retention time, in minutes.
markers: localisation for well known sub-cellular markers. QFeatures of
unknown location are encode as
For further details, install the
pRolocdata package and see
An object of class
data.frame with 3010 rows and 28 columns.
pRolocdata package: http://bioconductor.org/packages/pRolocdata/
A draft map of the mouse pluripotent stem cell spatial proteome Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS. Nat Commun. 2016 Jan 12;7:8992. doi: 10.1038/ncomms9992. PubMed PMID: 26754106; PubMed Central PMCID: PMC4729960.