An Equine Protein Atlas Highlights Synovial Fluid Proteome Dynamics during Experimentally LPS-Induced Arthritis

In human proteomics, substantial efforts are ongoing
to leverage
large collections of mass spectrometry (MS) fragment ion spectra into
extensive spectral libraries (SL) as a resource for data independent
acquisition (DIA) analysis. Currently, such initiatives in equine
research are still missing. Here we present a large-scale equine SL,
comprising 6394 canonical proteins and 89,329 unique peptides, based
on data dependent acquisition analysis of 75 tissue and body fluid
samples from horses. The SL enabled large-scale DIA-MS based quantification
of the same samples to generate a quantitative equine protein distribution
atlas to infer dominant proteins in different organs and body fluids.
Data mining revealed 163 proteins uniquely identified in a specific
type of tissue or body fluid, serving as a starting point to determine
tissue-specific or tissue-type-specific proteins. We showcase the
SL by highlighting proteome dynamics in equine synovial fluid samples
during experimental lipopolysaccharide-induced arthritis. A fuzzy
c-means cluster analysis pinpointed SERPINB1, ATRN, NGAL, LTF, MMP1,
and LBP as putative biomarkers for joint inflammation. This SL provides
an extendable resource for future equine studies employing DIA-MS.