ArticleJournal of proteome research2016
Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.
Article in Journal of proteome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed.
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- Reference Materials for Improving Reliability of Multiomics Profiling.Phenomics (Cham, Switzerland) · 2024Review
- A novel mitochondria-related core gene signature to predict the prognosis and evaluate tumour microenvironment in CESC single-cell validation.Journal of cellular and molecular medicine · 2024Article
- Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment.Communications biology · 2023Article
- Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics.Genome biology · 2023Article
- Amantadine Toxicity inToxics · 2023Article
- TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.Journal of proteome research · 2023Article
- Mouse Stromal Cells Confound Proteomic Characterization and Quantification of Xenograft Models.Cancer research communications · 2023Article
- Review
- Pan-cancer proteogenomic investigations identify post-transcriptional kinase targets.Communications biology · 2021Article
- Proteogenomic and metabolomic characterization of human glioblastoma.Cancer cell · 2021Article
- Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Integrative Transcriptomic, Proteomic and Functional Analysis Reveals ATP1B3 as a Diagnostic and Potential Therapeutic Target in Hepatocellular Carcinoma.Frontiers in immunology · 2021Article
- Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer.Cancers · 2020Review
- Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes.iScience · 2020Article
- Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.Cell reports. Medicine · 2020Article
- Article
- Recent advances in mass spectrometry based clinical proteomics: applications to cancer research.Clinical proteomics · 2020Review
Corrections and comments
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Authors and funding
35 authors.
Funding
Abstract
The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm ). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.