Sicherer, Scott H. et al. Food allergy: Epidemiology, pathogenesis, diagnosis, and treatment. J Allergy Clin Immunol, 133 (2), 291 - 307.e5. 10.1016/j.jaci.2013.11.020
Ready to start building a targeted method? Start by browsing allergens
The Allergen Peptide Browser is an interactive web tool for accelerated targeted method development utilizing published literature data along with in silico predictions. Peptide selection begins with the selection of food allergen e.g. peanut and protein e.g. Ara h 1, aided by interactive graphics conveying abundance information. Subsequently, peptides can be selected based on empirical data, in silico detection probability estimates, and/or physiochemical properties. Interactive rose plots highlight proteotypic peptides within the context of all tryptic peptides from a given protein, while physiochemical property filtering can be used to narrow the list of candidate peptides in the cases where little empirical data exists. Species specificity for each peptide is then presented based on BLAST query results of the NCBI non-redundant protein database, with warnings for instances where a peptide is not unique among food allergens. Finally, peptides can be added to a cart and exported in a comma separated value format amenable to importing into Skyline, an open-source MS software package designed to export a targeted method to a mass analyzer in native instrument format.
BLAST 2.2.31+ was used to to perform the peptide search. Only hits with 100% identity and no gaps were retained for a given peptide. Peptides associated with the same species but referencing a unique accession were grouped for easy visualization.
BLAST DB: Sep 20, 2016
We would like to thank the Vincent Coates Foundation Mass Spectrometry Laboratory at Stanford University for constructive discussions. This work was supported by a grant from the Simons Foundation (SFLIFE #288992 to Stephen R. Quake).
|Unique peptides detected||822|
|Allergenic proteins with MS data||65|
The database has been structured around proteins recognized by the International Union of Immunological Societies (IUIS) as food allergens and belonging to one of the “big 8” food allergens, namely peanut, milk, egg, soy, wheat, tree nuts, fish, and shellfish. Empirical peptide counts were generated from the aggregation of prior publications reporting allergenic peptides in MS experiments. Inclusion has been limited to studies performing in-solution digestion with trypsin, followed with electrospray ionization (ESI) MS due to their applicability to a standardized, multiplexed quantitative workflow using selected reaction monitoring (SRM). All types of mass analyzers have been included, which has the benefits of greater confidence for truly proteotypic peptides. A full list of the references is included under the reference section.
We facilitate the development of targeted mass spectrometry methods for allergen detection by providing a cart function for saving and exporting proteotypic peptides. Transition selection and optimization along with SRM data analysis can then proceed using Skyline software  developed for this purpose
 MacLean, B. et al., Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 26 (7): 966-968 10.1093/bioinformatics/btq054
Professor of Bioengineering, Stanford University
co-President, Chan Zuckerberg Biohub
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