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. 2014 Mar;14(6):763-73.
doi: 10.1002/pmic.201300398. Epub 2014 Feb 16.

The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research

Louise Bundgaard  1 , Stine Jacobsen, Mette A Sørensen, Zhi Sun, Eric W Deutsch, Robert L Moritz, Emøke Bendixen
Affiliations

The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research

Louise Bundgaard et al. Proteomics. 2014 Mar.

Abstract

Progress in MS-based methods for veterinary research and diagnostics is lagging behind compared to the human research, and proteome data of domestic animals is still not well represented in open source data repositories. This is particularly true for the equine species. Here we present a first Equine PeptideAtlas encompassing high-resolution tandem MS analyses of 51 samples representing a selection of equine tissues and body fluids from healthy and diseased animals. The raw data were processed through the Trans-Proteomic Pipeline to yield high quality identification of proteins and peptides. The current release comprises 24 131 distinct peptides representing 2636 canonical proteins observed at false discovery rates of 0.2% at the peptide level and 1.4% at the protein level. Data from the Equine PeptideAtlas are available for experimental planning, validation of new datasets, and as a proteomic data mining resource. The advantages of the Equine PeptideAtlas are demonstrated by examples of mining the contents for information on potential and well-known equine acute phase proteins, which have extensive general interest in the veterinary clinic. The extracted information will support further analyses, and emphasizes the value of the Equine PeptideAtlas as a resource for the design of targeted quantitative proteomic studies.

Keywords: Acute phase proteins; Animal proteomics; Equine; PeptideAtlas; Proteotypic peptides.

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Figures

Figure 1
Figure 1
A) Alignment of sequences assumed to represent two subgroups of equine SAA. EQ_1 represents SAA subgroup 1 (Q9N0Y1), EQ_2 represents SAA subgroup 2 (ENSECAP00000009324). The similarity of amino acids to the left of the arrow is 54%, compared to 88% for the rest of the sequences. Observed peptides are marked in bold. B1) Alignment of the equine SAA subgroup 1 with hepatically produced bovine SAA (BO_1) (P35541). The similarity of amino acids to the left of the arrow is 61%. B2) Alignment of the equine SAA subgroup 2 with extrahepatically produced bovine SAA (BO_2)(Q8SQ28). The similarity of amino acids to the left of the arrow is 81%. Signal peptides are marked in italic. For the horse they are presumed by comparison with bovine SAA. CLUSTAL 2.1 multiple sequence alignment (http://www.ebi.ac.uk/Tools/msa/clustalw2/) were used for alignment.
Figure 2
Figure 2
Comparison of N-terminal sequences of equine (EQ) and human fibrinopeptide Aα, Bβ, and γ. The known human sequence annotations are given below the human sequence. Observed equine peptides are shown in bold. Signal peptides are marked in italic. For the horse they are presumed by comparison with the human sequences. CLUSTAL 2.1 multiple sequence alignment (http://www.ebi.ac.uk/Tools/msa/clustalw2/) were used for alignment.
Figure 3
Figure 3
Graphical depiction of the most highly observed peptides for haptoglobin in each sample. The colour intensity of the square reflects the abundance of observations in the given sample, with white colour as no observation and black as very high abundance.
See this image and copyright information in PMC

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