Project PXD005971

PRIDE Assigned Tags:
Biological Dataset



Proteomic landscape of the primary somatosensory cortex upon sensory deprivation


We employed label free quantitative mass spectrometry to address experience-dependent changes in the proteome after sensory deprivation in the primary somatosensory cortex. Cortical column- and layer-specific tissue samples were collected from control animals, with all whiskers intact, and animals whose C-row whiskers were bilaterally plucked for 11-14 days.

Sample Processing Protocol

Pups were bilaterally spared or deprived off of their C-row whiskers between P12 and P23-P26. The whisker deprivation was repeated every third day to ensure that there was no regrowth of the whiskers. 400 ┬Ám thalamocortical slices were prepared. L4 and L2/3 were isolated from barrel cortical columns A-E under a microscope using a pulled patch pipette; tissue from columns A and B were pooled with tissue from columns E and D, respectively. Proteins were isolated in a SDS buffer, denatured with high urea and purified on a 30 kDa filter according to the so called FASP protocol. Digestion was done with trypsin and tryptic peptides were desalted on C18 StageTips. Peptides were seperated with an 25 cm C18 HPLC column and sequenced on a Orbitrap Tribrid Fusion mass spectrometer.

Data Processing Protocol

Raw data was analysed using MaxQuant version with match-between-runs, label-free quantification and intensity based absolute quantification (iBAQ) enabled. The RefSeq protein sequence database downloaded at 28-06-2016 was used to identify proteins.


Rik Lindeboom, Radboud Institute for Molecular Life Sciences
Michiel Vermeulen, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen - the Netherlands ( lab head )

Submission Date


Publication Date


Corresponding dataset(s) in other omics resources

GSE90929 (GEO, NCBI)




Orbitrap Fusion


Not available

Experiment Type

Shotgun proteomics


    Kole K, Lindeboom RGH, Baltissen MPA, Jansen PWTC, Vermeulen M, Tiesinga P, Celikel T. Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. Gigascience. 2017 6(10):1-10 PubMed: 29020746