hlpsms: hyperLOPIT PSM-level expression data

hlpsmsR Documentation

hyperLOPIT PSM-level expression data


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.




An object of class data.frame with 3010 rows and 28 columns.


The 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.

See Also

See QFeatures to import this data using the readQFeatures() function.

rformassspectrometry/QFeatures documentation built on March 26, 2023, 8:22 p.m.