Mass spectrometry datasets on TFEB proteostasis

TFEB-interacting proteins were determined through immunoprecipitation of TFEB from MLE-12 cells. We compared proteins identified on the TFEB-EGFP resin to the control resin to find candidate binding partners of TFEB. These experiments identified DCAF7 as a binding partner of TFEB. Phosphoproteomics analysis revealed phosphorylation sites in TFEB protein., Immunoprecipitation of TFEB
TFEB-EGFP expressing cells ore Empty vector control cells were precipitated with GFP-Trap magnetic resin (ChromoTek). Resin was washed and sent for mass spectrometry analysis. Samples were processed and analyzed by MSBioworks (Ann Arbor, MI). Briefly, samples were boiled at 100°C for 15 minutes in 60 μL of 1.5X LDS buffer. The beads were removed and half of each submitted sample was processed by SDS-PAGE using a 10% Bis-Tris NuPAGE gel (Invitrogen) with the MES buffer system. The mobility region was excised into 10 equal sized segments and in-gel digestion was performed on each using a robot (ProGest, DigiLab) with the following protocol: washed with 25 mM ammonium bicarbonate followed by acetonitrile, reduced with 10 mM dithiothreitol at 60°C followed by alkylation with 50 mM iodoacetamide at RT, digested with sequencing grade trypsin (Promega) at 37°C for 4 h, quenched with formic acid and the supernatant was analyzed directly without further processin..., # Mass spectrometry datasets on TFEB proteostasis.

Dataset DOI: [10.5061/dryad.p2ngf1w2s](10.5061/dryad.p2ngf1w2s)

## Description of the data and file structure

These datasets describe experiments to find binding partners and phosphorylation sites in TFEB. Binding partners were determined using Immunoprecipitation (IP) followed by mass spectrometry in MLE-12 cells. Phosphorylation sites in TFEB were determined by gel purification of TFEB from lysate derived from MLE-12 cells that were treated with carfilzomib (4 hour treatment at 1µM), or vehicle control.

### Files and variables

#### File: MSB29110IPTFEBBand\_08.mzML

**Description:** Immunoprecipitation of TFEB-GFP, processed mass spectrum provided in mzML format.

#### File: MSB29111IPEBand\_10.mzML

**Description:** Immunoprecipitation of Empty-Vector GFP (Control), processed mass spectrum provided in mzML format.

#### File: MSB29110IPTFEBBand\_08.raw

**Description:** Immunoprecipitation of TFEB-GFP, raw data (Thermo format)...,