Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics

Abstract

The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that control the composition of the plasma proteome, we developed a mass spectrometry-based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue-specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue-specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome dynamics.

The TLR2 Antagonist Staphylococcal Superantigen-Like Protein 3 Acts as a Virulence Factor to Promote Bacterial Pathogenicity in vivo

“…It is known that the biological background complexity can influence the detectability of low abundant peptides with SRM [45] . The liver proteome is more complex than the heart proteome, as determined in a protein atlas of mouse tissues [30] , which provides a technical explanation for the different detection limits depending on the mouse organ.…”

“…Peptides derived from purified SSL3 were analyzed with datadependent mass spectrometry (MS) to generate a spectral library as previously described [30] using a search database containing the SSL3 amino acid sequence (UniProtKB-Q2G0X7). From the spectral library, selected reaction monitoring MS (SRM-MS) assays for all detected SSL3 peptides were generated with Skyline [31] .…”

Mass spectrometry for the discovery of biomarkers of sepsis

“…This strategy is termed “SWATH MS” 100 . Dynamics of the blood plasma proteome during severe sepsis were characterized using SWATH-MS in mice infected with S. pyogenes 101 . A spectral library of proteins was created from plasma and organs in healthy mice, and the library was used to measure how surrounding tissues, organs, blood vessels, and cells influence the plasma composition (Figure 3).…”

“…However, biomarkers involved in vasodilation did not perform successfully in this system. Using DIA allows for the measurement of several biomarker groups and supports the future discovery of new biomarkers in blood plasma 101 .…”

The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH‐MS

“…Interpretation of SWATH spectra, however, requires reference to a spectral library of peptide sequence matching (including established m / z and LC retention time co‐ordinates), itself oft‐obtained from the outcomes of multiple DDA runs. Spectral libraries of notable depth are available for only a few species (or specialized cells/tissues)—including human, mouse, a few microbiota, drosophila and tomato, zebrafish, and yeast—that, at present, limits the breadth of uptake of SWATH.…”