The SARS-CoV-2 pandemic has abruptly illustrated the lack of pandemic preparedness. Therefore, health organisations as the WHO have recommended the development of a robust molecular screening platform for early detection and monitoring of the spread of pathogens through the population. This implies supplementing current diagnostic tests like nucleic acid amplification tests (NAATs) with tests targeting other biomolecules, like proteins. Therefore, infectious proteomics holds great promise as orthogonal test procedure. Our previous effort on SARS-CoV-2 already demonstrated that MS-based methods could be used as an alternative for diagnostic testing. Here, I propose to extend the assay by incorporating biomarker peptides for other pathogens, monitoring innate immunity and for serology testing. For the discovery phase, I will use a state of the art data independent acquisition (DIA) method i.e. Scanning SWATH. Next, I will introduce the use of peptide immuno-enrichment technology (SISCAPA). This uncouples the assay from the matrix while increasing the sensitivity into the attomole range and combined with automated sample preparation and peak detection, would enable throughputs up to 500 samples per day per MS instrument. Large-scale validation will be done on patient samples originating from the Severe Acute Respiratory Infections (SARI) surveillance network in collaboration with Sciensano.