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

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