Comprehensive PTM profiling with SCASP-PTM uncovers mechanisms of p62 degradation and ALDOA-mediated tumor progression.

IF 7.5 1区生物学 Q1 CELL BIOLOGY

Cell reports Pub Date : 2025-04-03 DOI:10.1016/j.celrep.2025.115500

Zhan-Peng Lin, Guohong Gan, Xiao Xu, Chengwen Wen, Xin Ding, Xiang-Yu Chen, Kaijie Zhang, Wen-Yu Guo, Mingxin Lin, Yu-Yang Wang, Xi Chen, Changchuan Xie, Jinling Wang, Minjie Li, Chuan-Qi Zhong

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引用次数: 0

Abstract

Multiple post-translational modification (PTM) proteomics typically combines PTM enrichment with multiplex isobaric labeling and peptide fractionation. However, effective methods for sequentially enriching multiple PTMs from a single sample for data-independent acquisition mass spectrometry (DIA-MS) remain lacking. We present SDS-cyclodextrin-assisted sample preparation (SCASP)-PTM, an approach that enables desalting-free enrichment of diverse PTMs, including phosphopeptides, ubiquitinated peptides, acetylated peptides, glycopeptides, and biotinylated peptides. SCASP-PTM uses SDS for protein denaturation, which is sequestered by cyclodextrins before trypsin digestion, facilitating sequential PTM enrichment without additional purification steps. Combined with DIA-MS, SCASP-PTM quantifies the proteome, ubiquitinome, phosphoproteome, and glycoproteome in HeLa-S3 cell samples, identifying serine 28 phosphorylation as a key driver of poly(I:C)-induced p62 degradation. This method also quantifies PTMs in clinical tissue samples, revealing the critical role of ALDOA K330 ubiquitination/acetylation in tumor progression. SCASP-PTM offers a streamlined workflow for comprehensive PTM analysis in both basic research and clinical applications.

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基于SCASP-PTM的PTM综合分析揭示了p62降解和aldoa介导的肿瘤进展机制。

多重翻译后修饰（PTM）蛋白质组学通常将PTM富集与多重等压标记和肽分离相结合。然而，数据独立获取质谱法（DIA-MS）仍然缺乏从单个样品中顺序富集多个PTMs的有效方法。我们提出了sds -环糊精辅助样品制备(SCASP)-PTM，这种方法可以实现多种ptm的无脱盐富集，包括磷酸肽、泛素化肽、乙酰化肽、糖肽和生物素化肽。SCASP-PTM使用SDS进行蛋白质变性，在胰蛋白酶消化前由环糊精隔离，方便连续的PTM富集而无需额外的纯化步骤。结合DIA-MS， SCASP-PTM定量了HeLa-S3细胞样品中的蛋白质组、泛素组、磷酸化蛋白质组和糖蛋白质组，确定了丝氨酸28磷酸化是poly（I:C）诱导的p62降解的关键驱动因素。该方法还量化了临床组织样本中的PTMs，揭示了ALDOA K330泛素化/乙酰化在肿瘤进展中的关键作用。SCASP-PTM为基础研究和临床应用中全面的PTM分析提供了一个简化的工作流程。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Cell reports CELL BIOLOGY-

CiteScore

13.80

自引率

1.10%

发文量

1305

审稿时长

77 days

期刊介绍： Cell Reports publishes high-quality research across the life sciences and focuses on new biological insight as its primary criterion for publication. The journal offers three primary article types: Reports, which are shorter single-point articles, research articles, which are longer and provide deeper mechanistic insights, and resources, which highlight significant technical advances or major informational datasets that contribute to biological advances. Reviews covering recent literature in emerging and active fields are also accepted. The Cell Reports Portfolio includes gold open-access journals that cover life, medical, and physical sciences, and its mission is to make cutting-edge research and methodologies available to a wide readership. The journal's professional in-house editors work closely with authors, reviewers, and the scientific advisory board, which consists of current and future leaders in their respective fields. The advisory board guides the scope, content, and quality of the journal, but editorial decisions are independently made by the in-house scientific editors of Cell Reports.