Table 2.

Computational evaluation of peptides selected for experimental verification

Peptide	Sequence
ORT49035.1_103_123	VDLRDAKGVQVGDGNVQINRF
AAS80314.1_349_385	SFNNLGSGDQFNTPGGTQNINKGGNEVSGGNFYGSVQF
AEB69175.1_5_29	KSRFDQRGQKVIGQQINVAGDATLP
RDW70414.1_382_421	GAPANNTSNSIQHNNSGSGHQNSGSGQQNIGTNTGSGQQ

Peptide	PCFG	pHMM	PLAAC	PASTA2	AmyloG	ArchC
	FPR$\downarrow$	FPR$\downarrow$	FPR$\downarrow$	[PEU]$\downarrow$	[0-1]$\uparrow$	[0-1]$\uparrow$
ORT49035.1_103_123	$\le$ 0.0004	< 0.0004	0.022	− 2.5	0.63	0.379
AAS80314.1_349_385	< 0.0004	< 0.0004	< 0.0004	− 1.6	0.78	0.555
AEB69175.1_5_29	0.007$-0.07$	< 0.0004	0.022	− 3.7	0.43	0.488
RDW70414.1_382_421	< 0.0004	$0.01-0.35$	<0.0004	− 0.9	0.26	0.599

Top: List of peptides selected for experimental verification. Bottom: results of computational methods. For PCFG, pHMM (both with score averaging) and PLAAC we provide FPR against NLReff at which at least a part of the peptide is detected; for PASTA2—Pasta Energy Units; for AmyloGram (AmyloG) and ArchCandy (ArchC)—score ranged from 0 to 1. Arrow indicates if higher or lower value is more positive. Values exceeding the default or suggested thresholds are shown in bold (the thresholds are $1e-2$ for PCFG, pHMM and PLAAC, -5 PEU for PASTA2, 0.5 for AmyloGram, and 0.56 for ArchCandy). For PCFG, we provide the range of values for grammars of different maximum number of symbols; For pHMM—the range of values for profiles made from different accurate MSAs