RT Journal Article
SR Electronic
T1 Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 301242
DO 10.1101/301242
A1 Alexander M Crowell
A1 Casey S Greene
A1 Jennifer J. Loros
A1 Jay C Dunlap
YR 2018
UL http://biorxiv.org/content/early/2018/08/17/301242.abstract
AB Motivation Decreasing costs are making it feasible to perform time series proteomics and genomics experiments with more replicates and higher resolution than ever before. With more replicates and time points, proteome and genome-wide patterns of expression are more readily discernible. These larger experiments require more batches exacerbating batch effects and increasing the number of bias trends. In the case of proteomics, where methods frequently result in missing data this increasing scale is also decreasing the number of peptides observed in all samples. The sources of batch effects and missing data are incompletely understood necessitating novel techniques.Results Here we show that by exploiting the structure of time series experiments, it is possible to accurately and reproducibly model and remove batch effects. We implement Learning and Imputation for Mass-spec Bias Reduction (LIMBR) software, which builds on previous block based models of batch effects and includes features specific to time series and circadian studies. To aid in the analysis of time series proteomics experiments, which are often plagued with missing data points, we also integrate an imputation system. By building LIMBR for imputation and time series tailored bias modeling into one straightforward software package, we expect that the quality and ease of large-scale proteomics and genomics time series experiments will be significantly increased.Contact alexander.m.crowell{at}gmail.com, jay.c.dunlap{at}dartmouth.edu