New Proteomic Signatures to Distinguish Between Zika and Dengue Infections

Abstract

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Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection

“…Data and analysis: We obtained the RAW files from Allgoewer et al (2021). The data had been collected in data-independent acquisition mode, comprising 124 patient and 20 quality control samples.…”

“…We prepared spectral libraries based on data acquired in data-dependent acquisition mode from pooled and fractionated serum samples of Zika and dengue patients (Allgoewer et al 2021) using the Pulsar search engine within Spectronaut 14. Settings included Trypsin/P digest, peptide length of 7 to 52 amino acids and up to two missed cleavages.…”

“… A) We analyzed 122 serum samples from 62 patients from Trinidad, diagnosed with dengue and Zika as published in Allgoewer (2021). B) Most peptides observed and with significant expression differences had one modification, but some had more.…”

“…Therefore, we tested the ability of existing data to help with prioritization of highly promising modifications for future analyses. Specifically, we examined a published mass spectrometry data set from 62 dengue and Zika patient serum samples (Allgoewer et al 2021) (Figure 1A) which had been acquired in data-independent acquisition (DIA) mode for protein abundance analysis. DIA methods are well suited for such analysis as they generate fragmentation spectra for all ions captured in the full scan and contain all their ion chromatograms, providing the quantification abilities of targeted analyses with an expanded coverage of proteins and enabling the re-mining of existing data (Rosenberger et al 2014; Faria et al 2017).…”

Pathogenesis and virulence of flavivirus infections

“…The majority of clinical proteomics studies to date have focussed on DENV disease progression. More recently unique protein signatures in patient serum were identified that could distinguish between ZIKV and DENV infection[ 225 ]. Thirteen differentially expressed proteins were identified, with 10 upregulated in ZIKV compared to DENV infection.…”