Table 3.

Iceman-specific amino acid substitutions detected in 4 proteins

UniProt accession	Protein name	No. of IDs (FDR 1 %/5 %)		AAS	Alignment Iceman vs. best BLAST hit
	Peptide sequence	FDR	RT (min)	%B	PPM	XCorr	Probability	Ions matched	In-solution	In-gel	Sample
Q13617	Cullin 2	4/2		E666D	TSMQKDTPQEMDQTR  –TSMQKDTPQEMEQTR–
	TSMQKDTPQEMDQTR	p ≤ 0.01	91	31	0.19	3.45	12.88	9/28	x	–	1024
	TSMQKDTPQEMDQTR	p ≤ 0.01	92	31	0.98	3.33	19.57	9/28	x	–	1025
	TSMQKDTPQEMDQTR	p ≤ 0.01	85	29	−0.47	3.28	7.03	8/28	x	–	1025
	TSMQKDTPQEMDQTR	p ≤ 0.05	85	29	−0.06	3.00	27.49	10/28	x	–	1025
	TSMQKDTPQEMDQTR	p ≤ 0.01	74	36	1.23	2.96	20.66	10/28	–	x	1024
	TSMQKDTPQEMDQTR	p ≤ 0.05	73	35	0.21	2.51	10.49	8/28	–	x	1025
Q3B820	Protein FAM161A isoform 2	2/0		I107 M	AHMETMAKLEKM  –AHIETMAKLEKM–
	AHM(ox)ETMAKLEKM(ox)	p ≤ 0.01	67	23	−1.51	2.80	28.28	9/22	x	–	1024
	AHM(ox)ETMAKLEKM(ox)	p ≤ 0.01	67	24	−0.11	2.66	25.90	8/22	x	–	1025
Q9H0T7	Ras-related protein Rab-17	0/2		V130 M	DLEEELHPGEVLVMLMGNK  –DLEEELHPGEVLVMLVGNK–
	DLEEELHPGEVLVMLMGNK	p ≤ 0.05	52	19	−1.36	2.69	12.78	14/72	x	–	1024
	DLEEELHPGEVLVMLMGNK	p ≤ 0.05	59	21	0.14	2.61	19.28	16/72	x	–	1025
O15018	PDZ domain-containing protein 2	0/1		G715D	SASPNFNTSGGASAGGSDEGSSSSLDR  –SASPNFNTSGGASAGGSDEGSSSSLGR–
	SASPNFNTSGGASAGGSDEGSSSSLDR	p ≤ 0.05	46	23	−3.99	2.82	18.26	12/104	–	x	1024

The upper two peptides were classified as higher confidence identifications based on the FDR and the number of PSM matches, the lower two were classified as candidates. The table contains the number of peptide identifications based on the FDR approach [No. of IDs (1 %/5 %)]; the retention time (RT) in minutes; the composition of the LC solution at the specific retention time (%B); the mass accuracy; the scores (XCorr and Probability); the number of matched versus theoretical expected ions in spectra; and their source of origin (In-gel or In-solution) and the sample itself (1024 or 1025). The corresponding MS/MS spectra are shown in the Supplementary Figure S12