SynthesisMolecular & cellular proteomics : MCP2011
Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ).
Synthesis in Molecular & cellular proteomics : MCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.Nature communications · 2023Article
- Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry.Journal of proteome research · 2023Article
- A statistical testing procedure for validating class labels.Journal of applied statistics · 2023Article
- Missing data in multi-omics integration: Recent advances through artificial intelligence.Frontiers in artificial intelligence · 2023Review
- Limited Proteolysis-Mass Spectrometry Reveals Aging-Associated Changes in Cerebrospinal Fluid Protein Abundances and Structures.Nature aging · 2022Article
- Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?Journal of proteome research · 2022Article
- Quantitative Proteomics Using Isobaric Labeling: A Practical Guide.Genomics, proteomics & bioinformatics · 2021Review
- Systematic detection of functional proteoform groups from bottom-up proteomic datasets.Nature communications · 2021Article
- Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation.Journal of proteome research · 2021Article
- Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences.Molecular & cellular proteomics : MCP · 2017Article
- Proteoform-Specific Insights into Cellular Proteome Regulation.Molecular & cellular proteomics : MCP · 2016Article
- DeMix-Q: Quantification-Centered Data Processing Workflow.Molecular & cellular proteomics : MCP · 2016Article
- Bayesian proteoform modeling improves protein quantification of global proteomic measurements.Molecular & cellular proteomics : MCP · 2014Article
- SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.Molecular & cellular proteomics : MCP · 2014Article
- Defining, comparing, and improving iTRAQ quantification in mass spectrometry proteomics data.Molecular & cellular proteomics : MCP · 2013Article
- Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.Nature communications · 2013Article
- Tumor proteomics by multivariate analysis on individual pathway data for characterization of vulvar cancer phenotypes.Molecular & cellular proteomics : MCP · 2012Article
- Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway.Nature communications · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a tool to improve quantitative accuracy and precision in mass spectrometry based on shotgun proteomics: protein quantification by peptide quality control, PQPQ. The method is based on the assumption that the quantitative pattern of peptides derived from one protein will correlate over several samples. Dissonant patterns arise either from outlier peptides or because of the presence of different protein species. By correlation analysis, protein quantification by peptide quality control identifies and excludes outliers and detects the existence of different protein species. Alternative protein species are then quantified separately. By validating the algorithm on seven data sets related to different cancer studies we show that data processing by protein quantification by peptide quality control improves the information output from shotgun proteomics. Data from two labeling procedures and three different instrumental platforms was included in the evaluation. With this unique method using both peptide sequence data and quantitative data we can improve the quantitative accuracy and precision on the protein level and detect different protein species.
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Registered trials
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.