ups {baldur} | R Documentation |
Spiked-in data set of peptides
Description
A dataset containing quantification of peptides using Progenesis. True
positives peptides spiked-in from the Universal Proteomics Standard Set 1
(UPS1) at three different concentrations and true negatives from
Chlamydomonas reinhardtii with the same concentration in all samples.
You can find true positives with stringr::str_detect(ups$identifier, 'UPS')
. For details see Berg et al. (2019) and
if you use this dataset please cite the same paper.
Usage
ups
Format
A data frame with 10599 rows and 13 variables:
- identifier
id column for features, true positives contains UPS and true negatives contains Cre
- fmol25_1,fmol25_2,fmol25_3,fmol25_4
Technical replicates with true positives spiked-in from 25 fmol UPS1 peptides
- fmol50_1,fmol50_2,fmol50_3,fmol50_4
Technical replicate with true positives spiked-in from 50 fmol UPS1 peptides
- fmol100_1,fmol100_2,fmol100_3,fmol100_4
Technical replicate with true positives spiked-in from 100 fmol UPS1 peptides
Source
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2619-6
References
Philip Berg, Evan W McConnell, Leslie M Hicks, Sorina C Popescu, George V Popescu (2019). “Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics.” BMC bioinformatics, 20(2), 7–16.