Project PXD001183

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Biomedical Dataset
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Proteomic characterisation of microtubule-dependent modulation of adhesion complexes


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.


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

Submission Date


Publication Date


Cell Type





Spectrum counting

Experiment Type

Shotgun proteomics

Assay count



    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


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