This document reproduces the Figures presented in (2016). For a description of the theory behind applications shown here we refer to the original manuscript. The results differ slightly due to technical changes or bugfixes in msqc1 that have been implemented after the manuscript was printed.
msqc1 1.28.0
Here we provide an experiment data package containing all the spread sheets used for figures and supplemental figures published in Kockmann et al. (2016). The raw instrument files are accessible for registered users through https://fgcz-bfabric.uzh.ch (2022) as project 1959. Raw LC-MS data from all five platforms were imported into Skyline 3.1, see MacLean et al. (2010), 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 Light:Heavy 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$relative.amount)
##
## 0.025 0.05 0.2 1 2 5
## 2550 2550 2550 2550 2550 2550
show the peptide frequency
table(msqc1_dil$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
## 378
show ion types
table(msqc1_dil$Fragment.Ion)
##
## b8 precursor precursor [M+1] precursor [M+2] y10
## 72 2106 2106 2106 720
## y11 y12 y4 y5 y6
## 144 144 396 990 1620
## y7 y8 y9
## 2106 1638 1152
show instruments
table(msqc1_dil$instrument)
##
## QExactive QExactiveHF QTRAP TRIPLETOF TSQVantage
## 3996 4032 1242 4032 1998