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Table 1 Parameters and variables involved in the SRM analytical chain model

From: Variance component analysis to assess protein quantification in biomarker validation: application to selected reaction monitoring-mass spectrometry

Notation Description Range
t Time  
t iln Discrete time sample n for peptide i and fragment l. In experimental conditions where only one ion by peptide is followed, this element is labeled only by peptide identifier i i = 1, …, S
l = 1, …, L
n = 1, …, N
d ip Digestion factor defined by the number of peptides i present in protein p i = 1, …, S
p = 1, …, P
g ip Digestion yield defined by the correction factor to apply to the digestion factor d ip to obtain ratio peptide/protein concentration i = 1, …, I
p = 1, …, P
ξ il Peptide to fragment gain i = 1, …, S
l = 1, …, L
\( {\phi}_{il}^{\ast } \) Peptide to fragment gain correction factor for AQUA peptide i = 1, …, S
l = 1, …, L
C i (τ i , λ i ) Normalized chromatography peak response of peptide i i = 1, …, S
τ i Chromatography peak position i = 1, …, S
λ i Chromatography peak width i = 1, …, S
I ikl (t il ) Transition signal at time t il i = 1, …, S
k = 1, …, K
l = 1, …, L
y p Protein p concentration p = 1, …, P
κ i Peptide i concentration before chromatography i = 1, …, S
ϱ ik Concentration of selected ion kof peptide i (precursor ion k of transition l) k = 1, …, K
ϑ kl Concentration of selected fragment lof selected ion k (fragment of precursor ion k of transition l) l = 1, …, L