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The lysate was first centrifuged at 14,000 rpm (27,000 g) at 4C for 10 min, and the resulting supernatant was centrifuged at 43,000 rpm (100,000 g) for 1 hr at 4C to further clarify the lysate. High speed supernatant was mixed with 500 l of GFP-coupled beads. and rotated for 1 hr at 4C to capture GFP-tagged proteins, then washed five times with 1 mL LAP200N buffer (200 mM KCl, 50 mM HEPES-KOH [pH 7.4], 1 mM EGTA, 1 mM MgCl2, 10% glycerol, protease inhibitors, and 0.05% NP40). After re-suspending the beads with 1 mL LAP200N buffer lacking protease inhibitors, the GFP tag was cleaved by adding 40 g PreScission-protease and rotating tubes at 4C for 16 hours. PreScission-protease eluted supernatant was added to 100 L of S-protein agarose (69704-3, EMD Millipore) to capture S-tagged protein. After washing three times with LAP200N buffer and twice with LAP0 buffer (50 mM HEPES-KOH [pH 7.4], 1 mM EGTA, 1 mM MgCl2, and 10% glycerol), purified protein complexes were eluted with 50 L of 2X LDS buffer and boiled at 95C for 3 min. Samples were then run on Bolt Bis- Tris Plus Gels (NW04120BOX, Thermo Fisher Scientific) in Bolt MES SDS Running Buffer (B0002, Thermo Fisher Scientific). Gels were fixed and stained according to Colloidal Blue Staining Kit (LC6025, Thermo Fisher Scientific) with Optima LC/MS grade water (W6-4, Fisher Scientific) at room temperature. The buffer was then replaced with Optima water prior to cutting the bands into eight pieces. The gel slices were then destained, reduced, and alkylated followed by in-gel digestion using (200 ng) Trypsin/LysC (V5073, Promega) as previously described. Tryptic peptides were extracted from the gel bands and dried in a speed vac. Prior to LC-MS, each sample was reconstituted in 0.1% formic acid, 2% acetonitrile, and water. Stage-Tips Clean Up: Homemade Stage-Tips were constructed using two C18 Empore disks, following established procedures. The fabricated Stage-Tips were subjected to a washing process, which involved two washes with 100 μL of methanol, one wash with 100 μL of 80% acetonitrile/0.1% acetic acid, and two washes with 100 μL of 1% acetic acid. Acidified peptides were loaded onto the Stage-Tips. Subsequently, the Stage-Tips were washed three times with 100 μL of 1% acetic acid to remove salts. Finally, the peptides were eluted from the Stage-Tips using two elution steps of 30 μL each, with 60% acetonitrile/0.1% acetic acid as the elution buffer. Liquid Chromatography Setup: A nanoELute ultra-high-pressure nano-flow chromatography system was utilized and directly coupled online with a hybrid trapped ion mobility spectrometry—quadrupole time-of-flight mass spectrometer (timsTOF Pro, Bruker) employing a nano-electrospray ion source (CaptiveSpray, Bruker Daltonics). Chromatographic Conditions: The liquid chromatography was conducted at a constant temperature of 50°C, employing a reversed-phase column (PepSep column, 10 cm × 150 μm i.d., packed with 1.5 μm C18-coated porous silica beads, Bruker) connected to the 10 μm emitter (Bruker). The mobile phase consisted of two components: Mobile Phase A, comprising water with 0.1/2% formic acid/ACN (v/v), and Mobile Phase B, comprising ACN with 0.1% formic acid (v/v). Gradient Elution: During the 60-minute experiments, peptide separation was achieved using a linear gradient from 2-33% Mobile Phase B within 60 minutes. This was followed by a washing step with 95% Mobile Phase B and subsequent re-equilibration. The chromatographic process maintained the flow rate at 400 nL/min. MS Acquisition: Samples were analyzed using the timsTOF HT Mass Spectrometer in DDA-PASEF mode. The TIMS elution voltage was calibrated linearly to obtain reduced ion mobility coefficients (1/K0) by using three selected ions from the Agilent ESI-L Tuning Mix (m/z 622, 922, 1222). The mass and ion mobility ranges were set from 100 to 1700 m/z and 0.7 to 1.3 1/K0, respectively. Both ramp and acquisition times were set at 100 ms. Precursor ions suitable for PASEF-MS/MS were chosen from TIMS-MS survey scans using the PASEF scheduling algorithm. A polygon filter was applied to the m/z and ion mobility plane to prioritize features likely representing peptide precursors over singly charged background ions. The quadrupole isolation width was set to 2 Th for m/z < 700 and 3 Th for m/z > 700, with collision energy linearly increased from 20 to 60 eV as ion mobility ranged from 0.6 to 1.6 (1/K0).PrideRaw mass spec result files were processed using Bionic (Protein Metrics, Inc.) software (version: 4.5.2) with the following parameters: precursor mass tolerance: 20 ppm, fragment mass tolerance: 40 ppm; fragmentation type: QTOF/HCD; carbamidomethyl as Cys fixed modification, variable modifications of Met oxidation, Asn and Gln deamidation, pyro-Glu formation at N-term Glu and Gln, N-term Acetylation and Ser, Thr and Tyr phosphorylation, with maximum 3 variable modification; trypsin with maximum 2 missed cleavages and fully specific mode; identifications were filtered at 0.01 FDR at the protein level; a fasta library of all human refseq proteins (curated and predicted) was used that was downloaded on 2021/07/20.ProteomicsPeter Kent JacksonCOMPLETEBaxter Laboratory for Stem Cell Biology Department of Microbiology & Immunology Stanford University School of MedicineHomo Sapiens (human)Not availablejdemeter@stanford.eduStanford UniversityUnited States10.6019/PXD055829falseTHE FAM53C/DYRK1A AXIS REGULATES THE G1/S TRANSITION OF THE CELL CYCLEA growing number of small molecules are becoming available to target the cell cycle machinery for the treatment of cancer and other human diseases. Consequently, a greater understanding of the factors regulating cell cycle progression becomes essential to help enhance to response of patients to these drugs. Here we identified the poorly-studied factor FAM53C as a new regulator of the G1/S transition. We first used data from the Cancer Dependency Map to identify new candidate regulators of the G1/S transition, and validated FAM53C as necessary and sufficient for this cell cycle transition. Genetic approaches showed that FAM53C acts upstream of the RB tumor suppressor. By mass spectrometry, we identified and validated DYRK1A as a kinase normally inhibited by FAM53C. DYRK1A is an upstream negative regulator of Cyclin D, which also negatively regulates RB. Fam53C knockout mice are viable but show defects in growth. Together, these experiments identify FAM53C as a regulator of DYRK1A and of cell cycle progression in 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