protRSA_test: Protein-level test data set, RSA profiles

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Protein-level test data set, RSA profiles

Description

RSA profiles. RSA refers to data expressed as relative specific amounts, which are ratios of two ratios: the numerator is the amount of a given protein in a particular fraction divided by the amount of that given protein in the starting material while the denominator is amount of total protein in a particular fraction divided by the amount of total protein in the starting material. The RSA describes the fold-enrichment (RSA>1) or depletion (RSA<1) of a protein during the fractionation process, and is analogous to the relative specific activity term used in classical analytical subcellular fractionation (see Tutorial 3). The test set was derived from TMT MS2 data from experiment AT5 of Tannous et al. and consists of mean profiles for proteins TLN1, TLN2, AIF1 and those listed in “markerListJadot”.

Usage

data(protRSA_test)

Format

A test data set

N

a numeric vector

M

a numeric vector

L1

a numeric vector

L2

a numeric vector

P

a numeric vector

S

a numeric vector

Nyc1

a numeric vector

Nyc2

a numeric vector

Nyc3

a numeric vector

Nspectra

a numeric vector

Npep

a numeric vector

Value

A test data set

References

Tannous, A.; Boonen, M.; Zheng, H.; Zhao, C.; Germain, C. J.; Moore, D. F.; Sleat, D. E.; Jadot, M.; Lobel, P., Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res 2020, 19, (4), 1718-1730.

Examples

data(protRSA_test)
str(protRSA_test)

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.