hlpsms: hyperLOPIT PSM-level expression data
In QFeatures: Quantitative features for mass spectrometry data
Description
Usage
Format
Source
References
See Also
Description
A 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 "unknown".
For further details, install the pRolocdata package and see
?hyperLOPIT2015.
Usage
1
Format
An object of class data.frame with 3010 rows and 28 columns.
Source
The pRolocdata package: http://bioconductor.org/packages/pRolocdata/
References
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.
See Also
See QFeatures to import this data using the readQFeatures() function.
QFeatures documentation built on Nov. 8, 2020, 6:51 p.m.
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Description Usage Format Source References See Also
Description
A 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
"unknown".
For further details, install the pRolocdata package and see
?hyperLOPIT2015.
Usage
1 |
Format
An object of class data.frame with 3010 rows and 28 columns.
Source
The pRolocdata package: http://bioconductor.org/packages/pRolocdata/
References
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.
See Also
See QFeatures to import this data using the readQFeatures() function.
R Package Documentation
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