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.

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