REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Patient plasma samples	Radboud UMC, the Netherlands	N/A
Healthy plasma samples	Radboud UMC, the Netherlands	N/A
Deposited data
Raw datafiles	This paper	http://www.proteomexchange.org/dataset/PXD028437
Software and algorithms
DataAnalysis v4.2	Bruker Daltonik GmbH, Germany	https://www.bruker.com
BioPharma Compass v3.0	Bruker Daltonik GmbH, Germany	https://www.bruker.com/en/products-and-solutions/mass-spectrometry/ms-software/biopharma-compass.html
KNIME v3.2.1	KNIME, USA	https://www.knime.com
KNIME OpenMS nodes v2.7.0	KNIME, USA	https://www.knime.com/community/bioinf/openms
OpenMS workflow	Wessels et al.16	http://www.proteomexchange.org/dataset/PXD034214
MATLAB 2014b	MatWorks, USA	https://www.mathworks.com/products/matlab.html
PERL	Perl, USA	https://www.perl.org/get.html
PLS-DA and GA-RF codes	Wessels et al.16	http://www.proteomexchange.org/dataset/PXD034214
ShinyGO v0.61 (Gene Ontology enrichment analysis)	Ge et al.40	http://bioinformatics.sdstate.edu/go/
Other
Patient metadata	This paper	Table S2, PXD028437