Contents

1 Introduction

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.

2 MSQC1 Peptide properties

2.1 Figure - reference L:H ratio versus the on-column amount

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.

3 Have fun with the data

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] 
##              72            2106            2106            2106 
##             y10             y11             y12              y4 
##             720             144             144             396 
##              y5              y6              y7              y8 
##             990            1620            2106            1638 
##              y9 
##            1152

show instruments

table(msqc1_dil$instrument)
## 
##   QExactive QExactiveHF       QTRAP   TRIPLETOF  TSQVantage 
##        3996        4032        1242        4032        1998

4 Graphics

4.1 Figure - Sigma mix peptide level signals