ArticleMolecular omics2021
Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes.
Article in Molecular omics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Baseline cellular state shapes the molecular impact of mutant Kirsten rat sarcoma viral oncogene homologue (KRAS) alleles in reconstituted pancreatic cancer cells.Molecular omics · 2026Article
- PI3K Regulates Wild-type RAS Signaling to Confer Resistance to KRAS Inhibition.Cancer research · 2026Article
- Hypovirus-Induced Phosphorylation of CpIre1 Modulates Unfolded Protein Response and Virulence in Cryphonectria parasitica.Molecular plant pathology · 2026Article
- DLX2 acts as a pioneer factor and drivesScience advances · 2026Article
- Divergent proteome tolerance against gain and loss of chromosome arms.Molecular cell · 2025Article
- A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy.Nature communications · 2025Article
- Article
- GABAMolecular cell · 2025Article
- An Extensive Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions.bioRxiv : the preprint server for biology · 2024Article
- Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2024Review
- EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling.Science advances · 2024Article
- The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8Nature communications · 2024Article
- SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data.NAR genomics and bioinformatics · 2023Article
- MSBooster: improving peptide identification rates using deep learning-based features.Nature communications · 2023Article
- Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.Nature communications · 2023Article
- An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.Nature communications · 2023Article
- Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer.Biophysics reports · 2023Article
- A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology.Biophysics reports · 2023Article
- Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry.Journal of proteome research · 2023Article
- Targeted Dephosphorylation of Tau by Phosphorylation Targeting Chimeras (PhosTACs) as a Therapeutic Modality.Journal of the American Chemical Society · 2023Article
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6 authors.
Funding
Abstract
Human cancer cell lines are widely used in pharmacological and systems biological studies. The rapid documentation of the steady-state gene expression landscape of the cells used in a particular experiment may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library-free data analysis workflow, to measure both the proteome and phosphoproteome of a melanoma cell line panel with different metastatic properties. For each cell line, the single-shot DIA-MS detected 8100 proteins and almost 40 000 phosphopeptides in the respective measurements of two hours. Benchmarking the DIA-MS data towards the RNA-seq data and tandem mass tag (TMT)-MS results from the same set of cell lines demonstrated comparable qualitative coverage and quantitative reproducibility. Our data confirmed the high but complex mRNA-protein and protein-phospsite correlations. The results successfully established DIA-MS as a strong and competitive proteotyping approach for cell lines. The data further showed that all subunits of the glycosylphosphatidylinositol (GPI)-anchor transamidase complex were overexpressed in metastatic melanoma cells and identified altered phosphoprotein modules such as the BAF complex and mRNA splicing between metastatic and primary cells. This study provides a high-quality resource for calibrating DIA-MS performance, benchmarking DIA bioinformatic algorithms, and exploring the metastatic proteotypes in melanoma cells.
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