Computational protocol: Quantitative Phosphoproteomics Reveals a Role for Collapsin Response Mediator Protein 2 in PDGF-Induced Cell Migration

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Protocol publication

[…] Details of the experimental setup for the quantitative phosphoproteomics experiments have been previously described. Within the MaxQuant output, phosphorylation sites were considered to be localised correctly if the localisation probability was at least 0.75 (75%) and the score difference at least 5. Significance testing was performed in the Perseus software environment, which is part of MaxQuant (Perseus version;, using a Student’s t-test on log 2 transformed ratios and controlled with a Benjamini-Hochberg FDR threshold of 0.05. Peptides quantified in three or more experimental repeats were deemed significantly changed and regulated by PDGF if they had a p-value of <0.05 and a ratio of <0.667 or >1.5 (at least a 1.5-fold change in abundance). The COMPARTMENTS database was used to assign proteins to subcellular localisations. Protein network visualization was performed using Cytoscape (version 3.3.0). DAVID (Database for Annotation, Visualization and Integrated Discovery) was used to identify over-represented KEGG pathways– (threshold count, 2; EASE score, 0.05) and REVIGO was used for identification and visualisation of over-represented GO terms. Kinases upstream of the identified PDGF-regulated phosphopeptides were predicted using Kinase Enrichment Analysis (KEA). […]

Pipeline specifications

Software tools MaxQuant, Perseus, DAVID, REViGO, KEA
Databases KEGG
Applications MS-based untargeted proteomics, Protein sequence analysis
Organisms Mus musculus
Chemicals Okadaic Acid