Here we provide an experiment data package containing all the spread sheets used for figures and supplemental figures published in [1]. The raw instrument files are accessible for registered users through http://fgcz-bfabric.uzh.ch as project 1959. Raw LC-MS data from all five platforms were imported into Skyline 3.1 [2], processed, and are available though https://panoramaweb.org/labkey/MSQC1.url when published. This package contains data.frame objects exported by Skyline making the data available for the R world.
The scatter-plot displays the reference L:H ratio versus the on-column amount of heavy peptide of the MSQC1 peptide mix. Note, x and y axis are drawn in log scale.
show the dilution series
table(msqc1_dil$relative.amount)##
## 0.025 0.05 0.2 1 2 5
## 2550 2550 2550 2550 2550 2550show the peptide frequency
table(msqc1_dil$Peptide.Sequence)##
## ADVTPADFSEWSK ALIVLAHSER AVQQPDGLAVLGIFLK DGLDAASYYAPVR
## 378 864 828 378
## EGHLSPDIVAEQK ESDTSYVSLK FEDENFILK FSTVAGESGSADTVR
## 1170 864 684 864
## GAGAFGYFEVTHDITK GAGSSEPVTGLDAK GGPFSDSYR GTFIIDPAAVIR
## 792 378 864 378
## GTFIIDPGGVIR GYSIFSYATK LFLQFGAQGSPFLK LGGNEQVTR
## 378 648 378 378
## NLSVEDAAR SADFTNFDPR TAENFR TPVISGGPYEYR
## 828 864 144 378
## TPVITGAPYEYR VEATFGVDESNAK VLDALQAIK VSFELFADK
## 378 378 864 864
## YILAGVENSK
## 378show ion types
table(msqc1_dil$Fragment.Ion)##
## b8 precursor precursor [M+1] precursor [M+2]
## 72 2106 2106 2106
## y10 y11 y12 y4
## 720 144 144 396
## y5 y6 y7 y8
## 990 1620 2106 1638
## y9
## 1152show instruments
table(msqc1_dil$instrument)##
## QExactive QExactiveHF QTRAP TRIPLETOF TSQVantage
## 3996 4032 1242 4032 1998
Sigma mix peptide level signals - The graph displays the log2 L:H area ratios of eight technical replicates over 14 peptides from five MS platforms. The 14 panels were ordered by the on column amount of heavy peptide per vial (0.8, 4, 20, 40, 80, 200, 500, 1000 fmol). The black line indicates the theoretical L:H ratio as reported in the QC certificate by Sigma-Aldrich. In a perfect setting all data points would be located close to the black line indicating a perfect match between theoretical and measured log2 L:H ratios. The dark gray boxes correspond to a 0.5 and the light grey boxes to a deviation of 1 from the expected value (black line).
S <- .shape_for_volcano(S=msqc1_8rep, peptides)
msqc1:::.figure_setup()
xyplot(-log(p.value, 10) ~ log2FC | instrument, data=S, group=Peptide.Sequence,
panel = function(...){
panel.abline(v=c(-1,1), col='lightgray')
panel.abline(h=-log(0.05,10), col='lightgray')
panel.xyplot(...)
},
ylab='-log10 of p-value',
xlab='log2 fold change',
layout=c(1,5),
auto.key = list(space = "right", points = TRUE, lines = FALSE, cex=1))
Ratio stability upon analyte dilution - Each scatter-plot panel displays the experimental derived log2 L:H ratios versus the relative amount. The panels are ordered by the SIL on column amount (lower left to upper right). Color grouping was done by instrument. The loess fit curves were added for visualizing the trend. The SIL value given in each panel legend is valid for the relative amount of 1. The horizontal black line indicates the theoretical log2 L:H ratio.
Accuracy - The graph displays in each panel a sensitivity curves for a given relative amount.
sessionInfo()## R version 3.4.0 (2017-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.5-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_1.4.0 lattice_0.20-35 BiocStyle_2.4.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.10 digest_0.6.12 rprojroot_1.2 grid_3.4.0
## [5] backports_1.0.5 magrittr_1.5 evaluate_0.10 stringi_1.1.5
## [9] rmarkdown_1.4 tools_3.4.0 stringr_1.2.0 yaml_2.1.14
## [13] compiler_3.4.0 htmltools_0.3.5 knitr_1.15.1[1] T. Kockmann, C. Trachsel, C. Panse, Åsa Wåhlander, N. Selevsek, J. Grossmann, W. E. Wolski, and R. Schlapbach, “Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective,” PROTEOMICS, 2016.
[2] B. MacLean, D. M. Tomazela, N. Shulman, M. Chambers, G. L. Finney, B. Frewen, R. Kern, D. L. Tabb, D. C. Liebler, and M. J. MacCoss, “Skyline: an open source document editor for creating and analyzing targeted proteomics experiments,” Bioinformatics, vol. 26, no. 7, pp. 966–968, Apr. 2010.