LCMS analysis with envipy

Transcription

1 LCMS analysis with envipy Uwe Schmitt Scientific IT Services ETH Zürich Uwe Schmitt

2 envipy graphical user interface Uwe Schmitt

3 envipy graphical user interface principles The graphical user interface: configures and controls workflow execution observes running workflow allows interactive inspection of intermediate and final results allows export of intermediate results to csv Uwe Schmitt

4 envipy sample inspector Uwe Schmitt

5 envipy peaklist inspection Uwe Schmitt

6 envipy workflow manager Multi core execution Always runs workflow from the beginning Caching of intermediate results Decoupled from user interface Headless execution on servers Every step attaches new information to peaks Uwe Schmitt

7 envipy workflow: peak picking envipick: fast peak picker for high resolution data Handles.raw,.mzML and.mzxml files Tested for Orbitrap and TOF data Assigns MS/MS data from data dependent measurements Uwe Schmitt

8 envipy workflow: isotope pattern computations envipat : fast and machine dependent calculation of isotope patterns Computes patterns of: Internal standards Targets Suspects Uwe Schmitt

9 envipy workflow: recalibration / alignment Reuses code from envimass m/z recalibration rt alignment Requires internal standards Uwe Schmitt

10 envipy workflow: peak shape fitting Asymmetric and symmetric peak shape models Raw area computation Uwe Schmitt

11 envipy workflow: screening Screening routine from envimass Matches precalculated isotope patterns to picked peaks Relaxed rt tolerances for suspect screening Uwe Schmitt

12 envipy workflow: component assignment Based on nontarget R package Assigns component id based on isotope, adduct and homologue relations Plus: m0 computation Uwe Schmitt

13 envipy workflow: time series analysis groups peaks over samples greedy algorithm for speed + reassignment from envimass: scoring of interesting time series Clustering of time series Event detection in time series Uwe Schmitt

14 envipy time series clustering based on affinity propagation algorithm No prior knowledge about number of expected clusters Similarity: correlation without mean normalization Uwe Schmitt

15 envipy workflow: event detection smoothing + detection of local maxima produce seeds Fit to gaussian profiles Uwe Schmitt

16 envipy workflow: MS/MS inspection The envipy peak picker extracts MS2 spectra from data dependent MS2 scans MS2 spectra can be exported as well as inspected in the envipy graphical user interface Uwe Schmitt

17 envipy MS/MS based identification Selected peaks with assigned MS/MS spectra can be identified by querying webservice Uwe Schmitt

18 envipy: availabilty Installer for Windows (includes R + Python) Requires 64bit Windows 7 or newer Faster with SSD drives Short release cycle, expect updates. Runs on Linux + Mac OS X (contact me for details) Uwe Schmitt

19 envipy: technical details Mostly Python 2.7 Reuses existing R code Starts R in separate process Communication over pipes Some speed optimizations in C (from Cython) Many functionalities from emzed ( Tables partly based on HDF5 PyQt4 for the graphical user interface Uwe Schmitt

20 Contact us Heinz Singer (EAWAG) Uwe Schmitt (ETH Zürich) Uwe Schmitt

21 Thank You