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Proteomic analysis of SPSB1 interactome

ABSTRACT: Flag-tagged SPSB1 was overexpressed in human 293FT cells followed by immunoprecipitation using ANTI-FLAG M2-Agarose Affinity Gel. The enriched SPSB1-interacting proteins on affinity gel were subject to quantitative proteomics analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: FURONG HUANG

LAB HEAD: Qianben Wang

PROVIDER: PXD057059 | Pride | 2026-06-29

REPOSITORIES: Pride

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			Action	DRS
	SPSB1_IP_rep1.mgf	Mgf
	SPSB1_IP_rep1.mzid.gz	Mzid
	SPSB1_IP_rep1.raw	Raw
	SPSB1_IP_rep2.mgf	Mgf
	SPSB1_IP_rep2.mzid.gz	Mzid

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1 - 5 of 24

Publications

Programmable mRNA 3'UTR engineering restores MHC-I and overcomes immune evasion in prostate cancer.

Huang Furong F Yuan Fuwen F Li Kexin K Cui Ya Y Li Lei L Ye Wenbin W Cui Zhifen Z Yan Jingyue J Chen Qiang Q Nicchitta Christopher C Zhang Yuebao Y Hankey William W Everitt Jeffrey J Huang Kai-Lieh KL Wang Mu-En ME Chen Ming M Huang Jiaoti J Wang Hongyan H Wagner Eric J EJ Lu Xin X Dong Yizhou Y Li Wei W Wang Qianben Q

Nature biomedical engineering 20260616

Immune-cold tumours such as prostate cancer often resist immune checkpoint therapies (ICT) due to impaired antigen presentation via major histocompatibility complex class I (MHC-I). While MHC-I downregulation is a common immune evasion mechanism, no approved therapies selectively restore MHC-I expression in tumours. We developed a programmable RNA engineering platform, termed the 3'UTR CRISPR/dCas13 Engineering System (3'UTRCES), to precisely manipulate mRNA alternative polyadenylation (APA) in ...[more]

PMID: 42303814

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Aurora A phosphorylates PKM2 at T45.

Project description:Flag-PKM2 was expressed in H1299 cells. Then the H1299 cells were treated with DMSO or 100nM MLN8237. Then, cell lysate was incubated with anti-Flag M2-agarose. Elutes were separated with 10% SDS-PAGE. The gel was stained with Coomassie Brilliant Blue. Visualized bands were excised and subjected to LC-MS/MS analysis. Then the phosphorylation sites of PKM2 were identified.

2023-03-11 | PXD036575 | Pride

Identification of GFI1 target genes in human lung adenocarcinoma cell line A549 [ChIP-seq]

Project description:To investigate the genes regulated by the transcription factor GFI1 in lung cancer cells, we overexpressed GFI1-Flag in A549 cells and performed ChIP-Seq with anti-Flag affinity gel.

2022-09-14 | GSE164984 | GEO

USP12-interacting proteins in A549 cells

Project description:The immunoprecipitates captured by Flag M2 affinity gel from USP12-Flag-expressed A549 cells were separated by SDS-PAGE. The gel was excised, digested with trypsin, and then subjected to LC-MS/MS analysis.

2021-07-09 | MSV000087785 | MassIVE

Archael ubiquitin-like SAMP3 is isopeptide-linked to Proteins by an UbaA-dependent mechanism

Project description:FLAG-SAMP3ylated proteins were immunoprecipitated from Haloferax volcanii using anti-FLAG affinity agarose and separated using SDS-PAGE. The Coomassie-stained IP-bands represented FLAG-SAMP3ylated proteins harvested from the wild type and also from the ubaA mutant as negative control. The Coomassie-lanes from the IP samples were cut into 10 fractions and in-gel tryptic digested and the tryptic peptides measured using Orbitrap Velos LC-MS/MS.

2020-07-02 | PXD000202 | Pride

BJ Flag-STING IP Mass Spectrometry

Project description:The goal of this project is to identify interacting proteins of Flag-tagged STING before and after cGAMP stimulation. STING knockout (STING-KO) BJ cells stably re-expressing Flag-STING were treated with 1 M cGAMP and whole cell lysates were harvested 30 min later for IP with anti-Flag M2 affinity gel. STING-KO cells without Flag-STING expression were used as a negative control.

2025-12-07 | PXD059426 | Pride

MRG15 interactome upon UV irradiation

Project description:The aim of this analysis is to identify the difference between interaction partners of MRG15 wild type and Chromodomain and MRG domain mutants upon UV irradiation. Therefore, MRG15 wild type and mutants (N-terminal FLAG tag) were overexpressed in U2OS cells. After UV irradiation, immunoprecipitation of the constructs was performed using FLAG M2 affinity gel. The constructs were eluted from the beads with 3xFLAG peptide.

2023-07-03 | PXD043089 | Pride

The inner nuclear membrane protein LEMD3-interacting proteins

Project description:HEK293T cells were transfected with the pcDNA3.1 or LEMD3-FLAG plasmid.Forty-eight hours after transfection, the cells were lysed in lysis buffer (50 mM Tris-HCl [pH=7.4], 150 mM NaCl, 2 mM EDTA, and 0.3% NP-40). The cell lysate samples were incubated with anti-FLAG M2 affinity gel (A2220, Sigma‒Aldrich) according to the manufacturer’s instructions. The anti-FLAG M2 affinity gel-bound proteins were eluted with FLAG peptide (F3290, Sigma). The final eluent was collected and resolved on an SDS-PAGE gel. The gel was fixed with a 30% ethanol:10% acetic acid solution, washed with 10% ethanol, and then subjected to LC‒MS/MS. Samples from HEK293T cells transfected with the pcDNA3.1 plasmid were used as the negative control.

2025-08-19 | PXD067510 |

Title: Identification of LEFKOTHEA/PORR protein partners

Project description:LEFKOTHEA (At5g62990) is a nuclear gene encoding an RNA-binding protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result to dual-targeting of LEFKOTHEA to the nucleus and chloroplasts. To identify the chloroplast and nuclear protein interactors of LEFKOTHEA, co-immunoprecipitation coupled to mass spectrometry (co-IP/MS) analysis was performed. The construct of LEFKOTHEA gene, expressed under the control of the endogenous promoter, with a FLAG tag at the C-terminus was introduced in Arabidopsis lefko2 mutant plants using the Agrobacterium system. The proteins were extracted under native conditions and incubated with anti-FLAG M2-agarose affinity gel. High salt concentrations and 3X FLAG peptide were applied to the beads for protein elution. The eluted protein fractions were subjected to Ultra High Pressure nanoLC-MS/MS. The LEFKOTHEA protein partners were identified using the MaxQuant software (version 1.5.3.30) against the complete Uniprot proteome of Arabidopsis thaliana (version of 19/1/2016) and a common contaminants database by the Andromeda search engine. Protein abundance was calculated on the basis of the normalized spectral protein intensity as label free quantitation (LFQ intensity). The statistical analysis was performed using Perseus (version 1.5.3.2).

2019-08-08 | PXD009965 | Pride

Human LC-MS, TMEM216 inhibits breast cancer lung metastasis by modulating IGF1R-IRS4 signaling pathway

Project description:Immunopurification and mass spectrometry analysis of TMEM216-associated proteins. Cellular extracts from Flag-TMEM216-expressing 293FT cells were affinity-purified. The eluates were resolved by SDS-PAGE and stained with Coomassie Brilliant Blue. The protein bands were retrieved and analyzed by mass spectrometry.

2026-05-31 | PXD061739 | Pride

Identification of the potential regulators of G6PD activity in different cell cycle

Project description:Flag-G6PD was expressed in HeLa cells. Then the HeLa cells were synchronized with a double thymidine block procedure. Briefly, the exponentially growing HeLa cells were maintained with 2 mM thymidine for 18 h, followed by a release of 9 h in fresh medium, and then cells were re-cultured in 2 mM thymidine for additional 15 h. These interphase cells were harvested. After a release of 8.5 h in fresh medium, the cells entered into M phase. Mitotic cells were harvested by mitotic shake-off. Then, cell lysate was incubated with anti-Flag M2-agarose. Elutes were separated with 10% SDS-PAGE. The gel was stained with Coomassie Brilliant Blue. Visualized bands were excised and subjected to LC-MS/MS analysis.

2023-05-18 | PXD033829 | Pride

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