TABLE 1.

Identification of prion proteins by tandem mass spectrometry

The amyloid identification procedure (TAPI) was performed on the isogenic yeast strain pair, 74D-694 [PSI+][RNQ+] and [psi-][rnq-]. The trypsin-treated fractions were analyzed using the in-house mass spectrometer (two left columns) or by commercial service (Keck Biotechnology Resource Laboratory at Yale University; two right columns). Samples with asterisks (*) were treated more thoroughly with SDS to remove the majority of ribosomal proteins (marked by italics). The hits are arranged by protein score. Bold type indicates known prion proteins.

74D[PSI+][RNQ+]		74D[psi-][rnq-]		74D[PSI+][RNQ+]*		74D[psi-][rnq-]*
Protein name	Protein score	Protein name	Protein score	Protein name	Protein score	Protein name	Protein score
Sup35	3123	RS11A	247	Sup35	1212	RL30	55
Rnq1	2042	RS11B	247	Rnq1	328	Tef3	46
RL27A	848	RL30	211	Nsr1	186	Ecm33	42
RL27B	848	RL27A	198	RS5	129	Cdc28	37
RL6A	540	RL27B	198	RL30	88	Vps5	37
RL6B	505	Pma1	194	RL10	87	Msc7	33
RL2B	373	Pma2	183	Cdc19	39	Ptc2	29
RL2A	373	RS3	140	Msc7	30	Ygr130c	26
RS9B	342	Tef1	115	Cdc28	26	Mnn9	21
RS9A	342	RL24A	102	Sis1	24
RL25	322	RL24B	102	Mnn9	21
RL4A	315	RS2	93	Faa4	21