Project PXD001183

PRIDE Assigned Tags:
Biomedical Dataset
Download Project Files
Project Protein Table
Project Peptide Table
Visualize in PRIDE Inspector
Follow the next three steps to open your selected project or assay in PRIDE Inspector:

  • 1.

    Download, uncompress and open PRIDE Inspector
  • 2.

    Click in the magnifier on the left top corner, paste the project or assay that you would like to open in the search box, and hit search
  • 3.

    Click in the corresponding "Download" button to download the files and visualize them

Summary

Title

Proteomic characterisation of microtubule-dependent modulation of adhesion complexes

Description

Investigating the effect of microtubule disruption by nocodazole treatment on isolated adhesion complexes.

Sample Processing Protocol

Adhesion complexes on fibronectin matrix were stabilised by DTBP cross-linking. Cells were lysed by sonication in an ammonium hydroxide buffer. Adhesion complexes were scrapped up in Laemmli reducing sample buffer, fractionated by SDS-PAGE, gel lanes cut into 30 slices and proteins were trypsin digested overnight. LC-MS/MS was carried out using a UltiMate 3000 RSLC, coupled to an Orbitrap Elite mass spectrometer. Peptides were concentrated on a pre-column (20 mm x 180 i.d, Waters) and separated in an analytical column (250mm x 75 um i.d 1.7 uM BEH C18 Waters).

Data Processing Protocol

Peak list files were searched against a modified version of IPI human database using an in-house Mascot server. Fixed modification was set for caramidomethylation of cysteine and variable modification was set for oxidation of methionine. Max missed clevages were set to 1. Mascot Daemon (v2.2) was used to process batched of RAW files by creating peak lists using extract_msn search script. Results were loaded in Scaffold 3, and peptide and protein identification threshold was set to 95% and 99% respectively.

Contact

Daniel Ng, The University of Manchester
Martin James Humphries, Wellcome Trust Centre for Cell-Matrix Research, University of Manchester ( lab head )

Submission Date

30/07/2014

Publication Date

30/01/2015

Cell Type

fibroblast

Modification

Oxidation
Carbamidomethyl

Quantification

Spectrum counting

Experiment Type

Shotgun proteomics

Assay count

8

Publication

    Ng DH, Humphries JD, Byron A, Millon-Frémillon A, Humphries MJ. Microtubule-dependent modulation of adhesion complex composition. PLoS One. 2014 Dec 19;9(12):e115213. eCollection 2014 PubMed: 25526367

Assay

Showing 1 - 8 of 8 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 38898 no assay title provided (mzIdentML) 2890 76652 7495 47791 47791
2 38899 no assay title provided (mzIdentML) 2949 85432 7572 50977 50977
3 38896 no assay title provided (mzIdentML) 3835 87467 7751 50160 50160
4 38897 no assay title provided (mzIdentML) 4185 86169 7948 48170 48170
5 38901 no assay title provided (mzIdentML) 3274 90223 8733 54394 54394
6 38900 no assay title provided (mzIdentML) 3379 87023 8971 51331 51331
7 38895 no assay title provided (mzIdentML) 3545 70137 5968 43246 43246
8 38894 no assay title provided (mzIdentML) 3865 64980 5879 39226 39226