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ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-Ctrl-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-NRAS-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-CFG4-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-APP-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-APP-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-CFG4-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-Ctrl-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-Ctrl-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-CFG4-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-NRAS-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-APP-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/RAPID-NRAS-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD070623/proteinGroups-Rapid-all_submission.xlsprimaryOK200yinsheng@ucr.edufeng tangData-dependent acquisitionMass SpectrometryBottom-up proteomicsG-quadruplexProteomicsLc-ms/msRna-protein interactionshttps://www.ebi.ac.uk/pride/archive/projects/PXD070623Cell CultureCell lines HEK293T cells were purchased from ATCC. All cell lines used in this study were tested to be free of mycoplasma contamination using LookOut Mycoplasma PCR Kit (Sigma, MP0035). Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin (v/v) at 37°C in a humidified incubator with 5% CO2. RaPID labeling was conducted by following previously published procedures with minor modifications20. Five million cells were seeded in T75 flasks the day before transfection. Plasmids for expressing motif RNA (10 g) and 2 μg of RaPID construct were co-transfected with 36 μL of Mirus TransIT-X2. The day after transfection, biotin (200 μM) was added to the culture media. Cells were incubated with 200 μM biotin for 2 hours and harvested as described below. Plasmids Motif RNA and RaPID plasmids were constructed following previously published procedures (Addgene plasmids #107250, 107251, 107252, 107253). To generate motif RNA plasmid, pairs of single-stranded DNA oligonucleotides encoding the motif RNA were annealed together to generate short double-stranded DNA fragments with 4 bp overhangs. These fragments were ligated into BsmBI-digested motif RNA plasmid. Primers for constructing RNA motif plasmids are listed in Table S4. RaPID-MS Cells were collected and lysed in CelLytic M cell lysis reagent (Sigma) with 1× protease inhibitor cocktail (Sigma). Pulldown of biotinylated proteins was performed with MyOne C1 Streptavidin Beads (Thermo Fisher) by following our previously reported procedures with minor modification35. One mg whole cell lysate was incubated with 30 μL beads in a rotator at 4°C for overnight. Beads were washed seven times with a series of buffers (1 mL each) to remove nonspecific binders: twice with RIPA lysis buffer, once with 1 M KCl, once with 0.1 M Na2CO3, once with 2 M urea in 10 mM Tris-HCl (pH 8.0), and twice with RIPA lysis buffer. The biotinylated proteins were eluted from the beads by boiling each sample in 30 μl of 3× protein loading buffer supplemented with 4 mM biotin and 20 mM DTT for 10 min. The resulting mixture was centrifuged, and the supernatant was loaded onto a 15% SDS-PAGE gel, which was run at 120 V for a very short duration (~10 min). The gel was washed to remove the running buffer and stained with Coomassie blue (VWR) for 30 min. The gel was subsequently destained overnight with a destaining solution (ethanol/H2O/acetic acid, 4.5:4.5:1, v/v). Gel slices containing the proteins were excised and cut into 1 mm2 cubes. The proteins were digested in-gel following a previously described protocol . Briefly, excess SDS in the gel was removed by incubating with 500 μL of 100 mM NH4HCO3/CH3CN (1:1, v/v) in a Thermo Mixer at 37°C with interval mixing at 1,200 rpm. The supernatant was removed and the gel pieces were dehydrated with acetonitrile for 5 min. Gel pieces were further dehydrated in a vacuum centrifuge for 1-2 min. Proteins were then reduced with 10 mM dithiothreitol (DTT, Sigma) in 25 mM NH4HCO3 at 55°C for 1 h, and subsequently alkylated by incubating with 55 mM iodoacetamide (IAA, Sigma) in the dark for 1 h. Gel pieces were dehydrated with acetonitrile and washed three times with 1 mL of 25 mM NH4HCO3. Proteins were then digested with trypsin at 37°C overnight. The peptides were subsequently eluted from the gel by incubating, with vigorous shaking at 37°C for 15 min, first in 200 μL of 5% formic acid (v/v) in 25 mM NH4HCO3, then in 200 μL of 5% formic acid in 25 mM NH4HCO3 and 50% acetonitrile (v/v), and finally in 200 μL of 5% acetic acid in 25 mM NH4HCO3 and 70% acetonitrile (v/v). the eluted peptide fractions were pooled, evaporated to dryness, desalted using OMIX C18 Tips (Agilent), and analyzed by LC-MS/MS. LC-MS/MS LC-MS/MS experiments were performed as previously described with minor modifications36. Briefly, the affinity pull-down samples were analyzed using an EASY-nLC 1200 system coupled with a Q Exactive Plus quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific). The HPLC separation was conducted using a trapping column followed by a separation column, both packed in-house with ReproSil-Pur C18-AQ resin (3 µm, Dr. Maisch HPLC GmbH, Germany). The peptides were separated using a 200-min linear gradient of 2-40% acetonitrile in 0.1% formic acid at a flow rate of 300 nL/min. The mass spectrometer was set up in the positive-ion mode, and the spray voltage was 1.8 kV. MS/MS were recorded in a data-dependent acquisition mode, in which one full-scan MS was followed with 25 MS/MS scans.PrideNot availableLC-MS/MS data were processed using MaxQuant version 1.6.14 with the default parameters unless otherwise specified (http://www.maxquant.org)37. Database search was performed using the Andromeda search engine included with MaxQuant with the UniProt human sequence database (UP000005640). The mass tolerances for precursor and fragment ions were set at 4.5 ppm and 20 ppm, respectively. Digestion enzyme specificity was set to trypsin with a maximum of 2 missed cleavages. A minimum peptide length of 7 residues was required for protein identification. N-terminal acetylation and methionine oxidation were set as variable modifications, and cysteine carboamidomethylation was set as a fixed modification. “Match between runs” based on accurate m/z and retention time was enabled with a 5-min alignment time window. Label-free quantitation (LFQ) was performed using the MaxLFQ algorithm in MaxQuant38. Protein LFQ intensities were calculated from the median of pairwise intensity ratios of peptides identified in two or more samples and adjusted to the cumulative intensity across samples. Quantification was performed using razor and unique peptides, including those modified by acetylation (protein N-terminus) and oxidation (Met). A minimum peptide ratio of 1 was required for protein intensity normalization. Data processing was performed using Perseus version 1.6.13.0 (http://www.perseus-framework.org). Protein group LFQ intensities were log2-transformed to reduce the effect of outliers. For statistical comparisons between proteomes, protein groups with missing LFQ values were assigned values using imputation. Missing values were assumed to be biased toward low-abundance proteins that were below the MS detection limit, referred to as “missing not at random”, an assumption that is frequently made in proteomics studies. The missing values were replaced with random values taken from a median downshifted Gaussian distribution to simulate low-abundance LFQ values. Imputation was performed separately for each sample from a distribution with a width of 0.3 and a downshift of 1.8. Differences in log2(LFQ intensity) were calculated between experimental and control groups. A two-tailed, unpaired, Student's t-test was employed to identify differentially enriched proteins. Visualization of the results was performed with volcano plots and Venn diagrams using the R libraries ggplot2 and VennDiagram. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE39 partner repositoryProteomicsYinsheng Wang1Department of Chemistry, University of California, RiversidePARTIALHomo Sapiens (human)41996289 Tang F, Liang X, Porter DF, Miao W, Maehlmann K, Yuan J, Khavari PA, Wang Y. Characterizations of G-Quadruplex RNA-Protein Interactions in Living Cells. Anal Chem. 2026 98(16):12090-12098 10.1021/acs.analchem.6c00902fengt@ucr.eduUniversity of California, riversideUnited StatesRNA guanine quadruplexes (rG4s) are noncanonical nucleic acid structures that contribute to diverse cellular functions and disease mechanisms. Defining the proteins that interact with rG4s (rG4IPs) is essential for elucidating their biological roles. Here, we build on the RNA-protein interaction detection (RaPID) platform to develop G4-RaPID, a tailored chemoproteomic strategy for the unbiased profiling of rG4IPs in living cells. Using G4-RaPID, we identified 105 candidate rG4IPs that were commonly enriched across three distinct rG4 sequences. Biochemical analyses confirmed that recombinant hnRNPA0, CHD4, and IGF2BP1 proteins directly bind rG4 structures in vitro. In addition, CLIP-seq experiments revealed significant enrichment of hnRNPA0 binding at endogenous rG4 loci. Luciferase reporter assays further demonstrated that hnRNPA0 engages the rG4 in the 5' UTR of NRAS mRNA to negatively regulate its translation. Together, these results establish G4-RaPID as a robust approach for mapping rG4-protein interactions in living cells and document hnRNPA0-rG4 recognition as a regulatory mechanism controlling NRAS mRNA translation.Characterizations of G-Quadruplex RNA-Protein Interactions in Living Cells.Tang Feng F, Liang Xiaochen X, Porter Douglas F DF, Miao Weili W, Maehlmann Kevin K, Yuan Jun J, Khavari Paul A PA, Wang Yinsheng YfalseCharacterizations of G-quadruplex RNA-Protein Interactions in Living CellsRNA guanine quadruplexes (rG4s) are non-canonical nucleic acid structures essential for various cellular functions and disease pathways. Characterizing rG4-interacting proteins (rG4IPs) is crucial for deciphering biological roles of rG4s. Building upon the RNA-protein interaction detection (RaPID) method, we introduced G4-RaPID – a tailored strategy for robustly profiling rG4IPs in living cells. Using G4-RaPID with three distinct rG4 sequences in live cells, we identified 105 candidate rG4IPs with diverse biological functions. We also validated the direct binding of recombinant hnRNPA0, CHD4, and IGF2BP1 proteins with rG4 structures in vitro. Additionally, our CLIP-Seq data revealed an enrichment of hnRNPA0 at rG4 loci. Moreover, luciferase reporter assay results showed that hnRNPA0 interacts with the rG4 in the 5UTR of NRAS mRNA to negatively regulate its translation. Together, we developed an rG4-RaPID method for characterizing rG4-protein interactions in living cells, and documented the functions of hnRNPA0-rG4 interaction in modulating the translation of NRAS 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