ArticleJournal of ocular biology, diseases, and informatics2009
Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses.
Article in Journal of ocular biology, diseases, and informatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
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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
94 citing papers in PubMed, 117 citations in OpenAlex.
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- Analysis of mouse lens morphological and proteomic abnormalities following deletion of the βB3-crystallin promoter.Experimental eye research · 2025Article
- Proteomic Characterization of the Rhesus Macaque Lens Nucleus: Similarity to Human Lens, Age Effects on Protein Solubility, and Trends in Post-Translational Modifications.Investigative ophthalmology & visual science · 2025Article
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- An engineered trafficking biosensor reveals a role for DNAJC13 in DOR downregulation.Nature chemical biology · 2025Article
- SMAP3-ID for Identification of Endogenous Protein-Protein Interactions Reveals Regulation of Mitochondrial Activity by Lamins.JACS Au · 2025Article
- DNAJC13 localization to endosomes is opposed by its J domain and its disordered C-terminal tail.bioRxiv : the preprint server for biology · 2024Article
- Electrical synapse molecular diversity revealed by proximity-based proteomic discovery.bioRxiv : the preprint server for biology · 2024Article
- Measurement of absolute abundance of crystallins in human and αA N101D transgenic mouse lenses usingExperimental eye research · 2024Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Analysis of shotgun proteomics datasets requires techniques to distinguish correct peptide identifications from incorrect identifications, such as linear discriminant functions and target/decoy protein databases. We report an efficient, flexible proteomic analysis workflow pipeline that implements these techniques to control both peptide and protein false discovery rates. We demonstrate its performance by analyzing two-dimensional liquid chromatography separations of lens proteins from human, mouse, bovine, and chicken lenses. We compared the use of International Protein Index databases to UniProt databases and no-enzyme SEQUEST searches to tryptic searches. Sequences present in the International Protein Index databases allowed detection of several novel crystallins. An alternate start codon isoform of betaA4 was found in human lens. The minor crystallin gammaN was detected for the first time in bovine and chicken lenses. Chicken gammaS was identified and is the first member of the gamma-crystallin family observed in avian lenses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9042-6) contains supplementary material, which is available to authorized users.
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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.