Table 1

Proteomics pipeline model summary

Parameters

Default values


No. of classes

2

Sample size of each class

M = 50

Proteome

Homo sapiens

No. of marker proteins

20

No. of non-markers

500

Protein block size

D = 2

Protein block correlation

ρ = 0.6

Fold change

al ~ Unif(1.5, 2)

Instrument response

κ = 5

Instrument saturation effect

sat = Inf

Noise level

α = 0.03, β = 3.6

Peptide efficiency factor

ei ~ Unif(0.1, 1)

Peptide detection algorithm

b = 0, k = .0016, p = 2

No. of MS2 replicates

1


Sun et al. BMC Genomics 2012 13(Suppl 6):S2   doi:10.1186/1471-2164-13-S6-S2

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