Table S1.

Shotgun MS of the Cas1–Cas2-3 complex

ID	Peptide counts (unique)	Protein name	Peptides	Unique peptides	Molecular mass, kDa	Length, amino acids	PEP	Coverage, %	Intensity	iBAQ
Q6D0W9	100	Cas2:3	91	91	124.89	1098	0	55.7	1.58E+11	2.14E+09
Q6D0X0	24	Cas1	23	23	36.258	326	0	39.6	7.26E+10	4.27E+09

ID: identifier(s) of the protein(s) contained in the protein group. Peptide counts (unique): number of peptides associated with each protein in the protein group. Here, distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide. Protein name: generic protein name(s) contained within the group. Peptides: total number of peptide sequences associated with the protein group (i.e., for all proteins in the group). Unique peptides: total number of unique peptides associated with the protein group (i.e., these peptides are not shared with another protein group). Molecular mass: molecular mass of the leading protein sequence contained in the protein group. Length: length of the leading protein sequence contained in the group. PEP: posterior error probability of the identification. This value essentially operates as a P value, where smaller is more significant. Coverage: percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group. Intensity: summed extracted ion current of all isotopic clusters associated with the identified amino acid sequence. iBAQ: values calculated by MaxQuant from the (raw) intensities taken into account by the number of theoretical peptides. Thus, iBAQ values are proportional to the molar quantities of the proteins. The iBAQ algorithm can roughly estimate the relative abundance of the proteins within each sample.