Computational protocol: The role and regulation of Rab40b–Tks5 complex during invadopodia formation and cancer cell invasion

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Protocol publication

[…] Putative Rab40b-binding proteins were identified using a GST–Rab40b affinity column as described previously (). Tandem mass spectra were analyzed via Sequest using a human, mouse and rat database concatenated to a randomized human, mouse and rat database. DTASelect was used to reassemble identified peptides into proteins. Identified proteins were filtered at a <5% false discovery rate. Proteins that were identified from GST–Rab40b eluate but were absent in GST-only eluate were considered as a candidate Rab40b-binding proteins and are listed in Fig. S3A. […]

Pipeline specifications

Software tools Comet, DTASelect
Application MS-based untargeted proteomics