REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Longitudinal plasma samples	Molecular Diagnosis and Risk Stratification of Sepsis (MARS) biorepository	ClinicalTrials.gov: NCT01905033
Longitudinal EDTA plasma samples from two healthy Caucasian donors	Precision Med (Solana Beach, CA, US)	7005-8200
Chemicals, peptides, and recombinant proteins
CaptureSelect™ FcXL affinity matrix	Thermo Fisher	194328010
FabALACTICA	Genovis	A0-AG1-020
Ni-NTA beads	Thermo Fisher	R90101
Trastuzumab	Roche, Penzberg, Germany	N/A
Alemtuzumab	Genmab, Utrecht, The Netherlands	N/A
Cetuximab, Rituximab, Bevacizumab, and Infliximab	Evidentic, Berlin, Germany	N/A
Oasis HLB	Waters Corporation, Milford, MA, USA	WAT058951
Deposited data
Bottom-up dataset – sequencing	This paper	https://doi.org/10.6084/m9.figshare.13194005
Middle-down dataset – sequencing	This paper	https://doi.org/10.6084/m9.figshare.13193996
Profiling LC-MS dataset	This paper	https://doi.org/10.6084/m9.figshare.13182743
Software and algorithms
BioPharmaFinder 3.2	Thermo Fisher	OPTON-30985
Pandas 1.2.4, Numpy 1.20.2, Scipy 1.6.2, Matplotlib 3.3.4, and Seaborn 0.11.1	McKinney, 2010; van der Walt et al., 2011; Virtanen et al., 2020; Hunter, 2007	N/A
PEAKS X	Bioinformatics Solutions Inc., Waterloo, ON, Canada	https://www.bioinfor.com/peaks-studio/
Xtract	Zabrouskov et al., 2005	N/A
ReSpect	Thermo Fisher Scientific, Bremen, Germany	N/A
DirecTag algorithm	Tabb et al., 2008	N/A
Thermo Proteome Discoverer (version 2.3.0.523)	Thermo Fisher Scientific, Bremen, Germany	OPTON-30945
Data analysis code	This paper	https://doi.org/10.6084/m9.figshare.14794173
Scripts used to generate the figures	This paper	https://doi.org/10.6084/m9.figshare.14794173
Other
MAbPac™ Reversed Phase HPLC Columns	Thermo Fisher	303184