ArticleBMC bioinformatics2012
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
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- Signaling pathways contributing to the transcriptional response to alkalinization in Komagataella phaffii: role of the transcription factors Crz1 and Rim101.Scientific reports · 2025Article
- Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine.Annual review of pharmacology and toxicology · 2024Review
- Human alveolar macrophages display marked hypo-responsiveness to IFN-γ in both proteomic and gene expression analysis.PloS one · 2024Article
- MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.Journal of proteome research · 2023Article
- Mena regulates nesprin-2 to control actin-nuclear lamina associations, trans-nuclear membrane signalling and gene expression.Nature communications · 2023Article
- BIRCH: An Automated Workflow for Evaluation, Correction, and Visualization of Batch Effect in Bottom-Up Mass Spectrometry-Based Proteomics Data.Journal of proteome research · 2023Article
- Human sperm proteome reveals the effect of environmental borne seminal polyaromatic hydrocarbons exposome in etiology of idiopathic male factor infertility.Frontiers in cell and developmental biology · 2023Article
- Article
- Proteomic profiling of human amnion for preterm birth biomarker discovery.Scientific reports · 2021Article
- Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial.Molecular systems biology · 2021Review
- Proteomic Alterations in Salivary Exosomes Derived from Human Papillomavirus-Driven Oropharyngeal Cancer.Molecular diagnosis & therapy · 2021Article
- Biomarkers of neonatal skin barrier adaptation reveal substantial differences compared to adult skin.Pediatric research · 2021Article
- Benchmarking Quantitative Performance in Label-Free Proteomics.ACS omega · 2021Article
- Heterogeneity in proline hydroxylation of fibrillar collagens observed by mass spectrometry.PloS one · 2021Article
- Cell-blocks and other ancillary studies (including molecular genetic tests and proteomics).CytoJournal · 2021Review
- Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer.Cancers · 2020Review
- Differential expression of the five redox complexes in the retinal mitochondria or rod outer segment disks is consistent with their different functionality.FASEB bioAdvances · 2020Article
- Global site-specific neddylation profiling reveals that NEDDylated cofilin regulates actin dynamics.Nature structural & molecular biology · 2020Article
- MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts.Mass spectrometry reviews · 2019Review
3 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
backgroundLiquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is widely used for quantitative proteomic investigations. The typical output of such studies is a list of identified and quantified peptides. The biological and clinical interest is, however, usually focused on quantitative conclusions at the protein level. Furthermore, many investigations ask complex biological questions by studying multiple interrelated experimental conditions. Therefore, there is a need in the field for generic statistical models to quantify protein levels even in complex study designs.
resultsWe propose a general statistical modeling approach for protein quantification in arbitrary complex experimental designs, such as time course studies, or those involving multiple experimental factors. The approach summarizes the quantitative experimental information from all the features and all the conditions that pertain to a protein. It enables both protein significance analysis between conditions, and protein quantification in individual samples or conditions. We implement the approach in an open-source R-based software package MSstats suitable for researchers with a limited statistics and programming background.
conclusionsWe demonstrate, using as examples two experimental investigations with complex designs, that a simultaneous statistical modeling of all the relevant features and conditions yields a higher sensitivity of protein significance analysis and a higher accuracy of protein quantification as compared to commonly employed alternatives. The software is available at http://www.stat.purdue.edu/~ovitek/Software.html.
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