Contents

1 Preliminaries

ssrc (Sequence Specific Retention Calculator) is an implementation of the algorithm proposed in [1] to predict the Retention Time (RT) of a given peptide sequence.

load libraries

an basic example from the paper …

lapply(c("SCHTAVGR", "SCHTGLGR", "EDLIAYLK"), ssrc)
## [[1]]
## SCHTAVGR 
##  3.20805 
## 
## [[2]]
## SCHTGLGR 
##  5.95145 
## 
## [[3]]
## EDLIAYLK 
## 29.60045

in the following paragraphs we will play with some R packages containing peptide sequence and RT information.

define a R-helper function which derives a linear model and visualize the result

.plot.rt_ssrc <- function(x, y, ...){
  fit <- lm(y~x)
  plot(x, y, ylab='ssrc predicted RT', xlab='RT',
       cex=2,
       asp=1,
       ...)
  
  abline(fit)
  abline(a=0, b=1, col='grey', lwd=2)
  
  legend("topleft", 
         c(paste("spearman", round(cor(x, y, method='spearman'),2)),
           paste('R-squared', round(summary(fit)$r.squared,2)))
         )
} 

2 Example 1 - using specL

3 Example 2 - using msqc1 peptides

library(msqc1)
## Loading required package: lattice

fetch the msqc1

msqc1.8rep.aggregate <- msqc1:::.reshape_rt(msqc1_8rep, peptides=peptides, plot=FALSE)
msqc1.dilution.aggregate <- msqc1:::.reshape_rt(msqc1_dil, peptides=peptides, plot=FALSE)

predict RT

msqc1.peptide.ssrc <- unlist(lapply(as.character(msqc1.dilution.aggregate$Peptide.Sequence), ssrc))

3.1 8replicate data

3.2 Dilution Series data

4 Session information

sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.8-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] msqc1_1.10.0     lattice_0.20-38  knitr_1.21       specL_1.16.1    
## [5] seqinr_3.4-5     RSQLite_2.1.1    protViz_0.4.0    DBI_1.0.0       
## [9] BiocStyle_2.10.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.0         magrittr_1.5       MASS_7.3-51.1     
##  [4] bit_1.1-14         stringr_1.3.1      blob_1.1.1        
##  [7] highr_0.7          tools_3.5.2        grid_3.5.2        
## [10] parallel_3.5.2     xfun_0.4           htmltools_0.3.6   
## [13] yaml_2.2.0         bit64_0.9-7        ade4_1.7-13       
## [16] digest_0.6.18      bookdown_0.9       BiocManager_1.30.4
## [19] codetools_0.2-16   memoise_1.1.0      evaluate_0.12     
## [22] rmarkdown_1.11     stringi_1.2.4      compiler_3.5.2    
## [25] pkgconfig_2.0.2

References

[1] O. V. Krokhin, R. Craig, V. Spicer, W. Ens, K. G. Standing, R. C. Beavis, and J. A. Wilkins, “An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS,” Mol. Cell Proteomics, vol. 3, no. 9, pp. 908–919, Sep. 2004.