autoQC01 - Biognosys iRT peptides runs (old)

Summary | Status

Last entries

autoQC01

autoQC03 DDA

autoQC03 DIA

autoQC03 DDA - nConfidentPeptides.value ~ time | Instrument

graphs the number of confident peptides for each instrument over time.
Entries are reverse sorted by date.

Overview: Instrument ~ time | method

Each dot represents an LC-MS QC run.

Frequency

Graphs monthly number of LC-MS QC runs for each instrument and method.

README

The fgczqcms R package contains shell scripts and a shiny dashboard for handling mass spec qc workflows (dia, dda) for Orbitrap and timsTof devices.

data are preprocessed as follow:

pre-processing

autoQC01

  • compute host: cpanse@fgcz-c-072:/scratch/FGCZ-MS-QC-DASHBOARD_A331/qc running
while true;
do 
  clear; date;
  make -f Makefile.autoQC01 ;
  sleep 60;
done

for

  • Thermo Orbitrap (QEXACTIVE_1|…)

autoQC03dda

  • compute host: running @fgcz-r-033
# autoQC03dda AUTOQC4L TIMSTOF
37 * * * * (/scratch/cpanse/timstof/bin/fgcz_timsTOF_autoQC4L.bash   2>&1)  >> /home/cpanse/data/runme_autoQC4L_TIMSTOF_1.log 
17 * * * * (/scratch/cpanse/timstof/bin/fgcz_TIMSTOFFLEX_1_autoQC03dda.bash 2>&1) >> /home/cpanse/data/runme_autoQC4L_TIMSTOFFLEX_1.log 

*/29    *       *       *       *     ( nice -19 /home/cpanse/__projects/2019/20190225-comet/runme_autoQC4L_comet.bash ) 2>/tmp/autoQC4L.2.log > /tmp/autoQC4L.1.log

TODO(cp): this script requires refactoring: /home/cpanse/__projects/2019/20190225-comet/runme_autoQC4L_comet.bash

  • Thermo Orbitrap (QEXACTIVE_1|…)
  • Bruker timsTOF

see also:

autoQC03dia

  • compute host: cpanse@fgcz-c-072:/scratch/FGCZ-MS-QC-DASHBOARD_A331/qc
while true;
do 
  clear;
  date;
  make -f Makefile.DIANN stageinput \
    && make -f Makefile.DIANN convert \
    && make -f Makefile.DIANN diann \
    && make -f Makefile.DIANN output ;
    sleep 60;
done
  • Thermo Orbitrap (QEXACTIVE_1|…)
  • Bruker timsTOF (TIMSTOF_1|TIMSTOFFLEX_1)

contact

Email: cp@fgcz.ethz.ch

Session | debug - information