Table 1.
SEQUEST-derived protein identifications from mock and PrPSc samples. All proteins listed had at least two unique peptides derived from MS/MS spectra passing discriminate score cutoffs as described in the methods section. Keratin and trypsin sequences were filtered from the list. The total number of assigned spectra and the number of unique peptides (e.g, the number of peptides with distinct m/z values) were cumulatively tabulated from all of the samples examined. Proteins are listed in order of relative apparent abundance based upon spectral counts for the each of the proteins listed.
| Protein (Swiss-prot) | Spectral Count | Unique Peptides | 22L-06 | 22L-09A | 22L-09B | CH-04 | CH-06 | Mock |
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| Major Prion protein (P04925) | 1639 | 61 | √ | √ | √ | √ | √ | |
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| Ferritin light chain 1 (P29391) | 946 | 30 | √ | √ | √ | √ | √ | √ |
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| Ferritin heavy chain (P09528) | 867 | 35 | √ | √ | √ | √ | √ | √ |
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| Versican core protein (Q62059) | 94 | 14 | √ | √ | √ | |||
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| Myelin-associated oligodendrocyte basic protein (Q9D2P8) | 90 | 6 | √ | √ | √ | √ | ||
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| Hyaluronan and proteoglycan link protein 2 (Q9ESM3) | 80 | 17 | √ | √ | ||||
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| Proteasome subunit beta type-5 (O55234) | 74 | 11 | √ | |||||
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| Apolipoprotein E (P08226) | 63 | 7 | √ | √ | √ | √ | ||
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| Collagen alpha-1(I) chain (P11087) | 56 | 2 | √ | √ | √ | √ | ||
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| Proteasome subunit beta type-2 (Q9R1P3) | 43 | 7 | √ | |||||
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| Ca/calmodulin-dependent protein kinase type II α chain (P11798) | 42 | 7 | √ | √ | √ | √ | √ | |
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| Proteasome subunit beta type-4 (P99026) | 38 | 5 | √ | |||||
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| Proteasome subunit beta type-1 (O09061) | 33 | 7 | √ | |||||
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| Proteasome subunit alpha type-7 (Q9Z2U0) | 29 | 7 | √ | √ | ||||
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| Myelin proteolipid protein (P60202) | 26 | 3 | √ | √ | √ | |||
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| Proteasome subunit beta type-3 (Q9R1P1) | 22 | 5 | √ | |||||
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| Hyaluronan and proteoglycan link protein 1 (Q9QUP5) | 21 | 8 | √ | |||||
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| 60S ribosomal protein L35 (Q6ZWV7) | 19 | 3 | √ | √ | √ | √ | √ | √ |
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| Ca/calmodulin-dependent protein kinase type II β chain (P28652) | 15 | 4 | √ | √ | √ | √ | ||
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| Proteasome subunit alpha type-6 (Q9QUM9) | 13 | 5 | √ | |||||
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| Proteasome subunit alpha type-4 (Q9R1P0) | 11 | 6 | √ | |||||
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| Proteasome subunit alpha type-2 (P49722) | 10 | 5 | √ | |||||
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| Proteasome subunit beta type-6 (Q60692) | 10 | 3 | √ | |||||
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| Myelin-oligodendrocyte glycoprotein (Q61885) | 8 | 2 | √ | √ | ||||
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| Junction plakoglobin (Q02257) | 8 | 4 | √ | √ | √ | √ | ||
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| 60S ribosomal protein L13a (P19253) | 6 | 2 | √ | √ | √ | √ | ||
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| Actin, cytoplasmic 1 (P60710) | 6 | 5 | √ | √ | ||||
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| Beta-actin-like protein 2 (Q8BFZ3) | 5 | 4 | √ | |||||
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| Ras-related protein Rab-3D (P35276) | 4 | 2 | √ | |||||
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| 60S ribosomal protein L3 (P27659) | 3 | 2 | √ | |||||
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| Claudin-11 (Q60771) | 3 | 3 | √ | √ | ||||