ArticleJournal of proteome research2011
Protein database and quantitative analysis considerations when integrating genetics and proteomics to compare mouse strains.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
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- The human tubal lavage proteome reveals biological processes that may govern the pathology of hydrosalpinx.Scientific reports · 2019Article
- The human brainome: network analysis identifies HSPA2 as a novel Alzheimer’s disease target.Brain : a journal of neurology · 2018Article
- Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue.Molecular & cellular proteomics : MCP · 2017Article
- Tag-Count Analysis of Large-Scale Proteomic Data.Journal of proteome research · 2016Article
- Proteomic Analysis of Non-depleted Serum Proteins from Bottlenose Dolphins Uncovers a High Vanin-1 Phenotype.Scientific reports · 2016Article
- A multi-model statistical approach for proteomic spectral count quantitation.Journal of proteomics · 2016Article
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- Accurate label-free protein quantitation with high- and low-resolution mass spectrometers.Journal of proteome research · 2014Article
- Correlation of actin crosslinker and capper expression levels with stereocilia growth phases.Molecular & cellular proteomics : MCP · 2014Article
- Proteomic approaches and identification of novel therapeutic targets for alcoholism.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2014Review
- A quantitative proteomic workflow for characterization of frozen clinical biopsies: laser capture microdissection coupled with label-free mass spectrometry.Journal of proteomics · 2012Article
- A systems approach implicates nuclear receptor targeting in the Atp7b(-/-) mouse model of Wilson's disease.Metallomics : integrated biometal science · 2012Article
- Distinct energy metabolism of auditory and vestibular sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Decades of genetics research comparing mouse strains has identified many regions of the genome associated with quantitative traits. Microarrays have been used to identify which genes in those regions are differentially expressed and are therefore potentially causal; however, genetic variants that affect probe hybridization lead to many false conclusions. Here we used spectral counting to compare brain striata between two mouse strains. Using strain-specific protein databases, we concluded that proteomics was more robust to sequence differences than microarrays; however, some proteins were still significantly affected. To generate strain-specific databases, we used a complete database that contained all of the putative genetic isoforms for each protein. While the increased proteome coverage in the databases led to a 6.8% gain in peptide assignments compared to a nonredundant database, it also necessitated the development of a strategy for grouping similar proteins due to a large number of shared peptides. Of the 4563 identified proteins (2.1% FDR), there were 1807 quantifiable proteins/groups that exceeded minimum count cutoffs. With four pooled biological replicates per strain, we used quantile normalization, ComBat (a package that adjusts for batch effects), and edgeR (a package for differential expression analysis of count data) to identify 101 differentially expressed proteins/groups, 84 of which had a coding region within one of the genomic regions of interest identified by the Portland Alcohol Research Center.
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