recycleLightLysine: Data frame with miss cleaved peptides quantifications from...
In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description Usage Format Details References

A data.frame that contains the output from searching heavy label incorporation as amino acid modifications. This search was done using the same data as in the wormsPE data.

1	data(recycleLightLysine)

A data.frame

Sequence: Column used as id to match with the peptides in the wormsPE ProteomicsExperiment.
Modifications: Column indicating how many heavy isotopes the peptide has.
Intensity.*: Columns containing quantification data in each sample.
...: Other columns containing peptide related information.

The reason why the search was done using isotopes as modifications is because MaxQuant only looks for peptides in which all amino acids are isotope labelled, miss-cleaved amino acids that contain an isotope mix are not measured by the normal silac search engine. This allows to find peptides which a mix of incoporated isotopes.

This dataset is used as an example, in the pulsed silac vignette, to estimate the amount of old isotope label in newly synthesized proteins (amino acid recycling).

https://www.ncbi.nlm.nih.gov/pubmed/28679685

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.