protNSA_AT5tmtMS2: Protein mean NSA values from the TMT-MS2 data, Expt AT5

In mooredf22/protlocassign0p1p1: Compute constrained proportional assignments for fractionated protein abundance

Description

Each of the 7893 genes (proteins) has relative abundance levels in the channels N, M, L1, L2, P, S, Nyc1, Nyc2, and Nyc3, constrained to sum to 1. Details may be found in A. Tannous et al. (2020). These levels refer to the relative levels measured by the mass spectrometer, averaged across spectra and peptides for each gene. They are not adjusted for protein amounts derived from the original samples.

Format

A data frame with 7893 observations on the following 12 variables.

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

Details

Nspectra is a count of the total number of spectra for each protein, and Npep is the number of peptides for that protein.

Source

Tannous A, Boonen M, Zheng H, Zhao C, Germain C, Moore D, Sleat D, Jadot M, Lobel P. Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. Journal of Proteome Research 2020, in press

References

Jadot M, Boonen M, Thirion J, Wang N, Xing J, Zhao C, Tannous A, Qian M, Zheng H, Everett JK, Moore DF, Sleat DE, and Lobel P (2016) Accounting for protein subcellular localization: a compartmental map of the rat liver proteome. Molecular and Cellular Proteomics 16, 194-212. doi:10.1074/mcp.M116.064527 PMCID: PMC5294208

Tannous A, Boonen M, Zheng H, Zhao C, Germain C, Moore D, Sleat D, Jadot M, Lobel P. Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. Journal of Proteome Research 2020, in press

Examples

head(protNSA_AT5tmtMS2)

mooredf22/protlocassign0p1p1 documentation built on Feb. 7, 2022, 1:55 a.m.