Table 1.

Overview of the datasets and processing steps used in this study.

Dataset	Pride Archive	Organism	Original Format	Mass Spectrometer	Frag Type	PrecTol	FragTol
MouseCID	PXD000790	M. musculus	MGF	LTQ Orbitrap Elite	CID	5 ppm	0.50 Da
YeastCID	PXD002726	S. cerevisiae	MGF	LTQ Orbitrap Velos	CID	10 ppm	0.80 Da
EcoliCID	PXD016825	E. coli	RAW	LTQ Orbitrap Velos	CID	20 ppm	0.50 Da
StaphAurCID	PXD017932	S. aureus	RAW	LTQ Orbitrap Velos	CID	5 ppm	0.60 Da
HeLaHCD	PXD000674	H. sapiens	RAW	Q Exactive	HCD	10 ppm	0.02 Da
PyroHCD	PXD001077	P. furiosus	RAW	LTQ Orbitrap Velos	HCD	10 ppm	0.06 Da
EcoliHCD	PXD008685	E. coli	MGF	Q Exactive	HCD	10 ppm	0.02 Da
StaphAurHCD	PXD023039	S. aureus	RAW	Q Exactive	HCD	10 ppm	0.06 Da

Frag Type: Fragmentation Type.

PrecTol: Precursor Mass Tolerance.

FragTol: Fragment Mass Tolerance.