SLIDE 1
Integrating experimental knowledge Michael Witting, Research Unit - - PowerPoint PPT Presentation
Integrating experimental knowledge Michael Witting, Research Unit - - PowerPoint PPT Presentation
Integrating experimental knowledge Michael Witting, Research Unit Analytical BioGeoChemistry, HMGU Dagstuhl Seminar Computational Metabolomics 1.12.2015 Experimental Knowledge Know your toolbox! Know your system! Know your
SLIDE 2
SLIDE 3
Experimental Knowledge
- Know your toolbox!
- Know your system!
- Know your organism!
(or at least ask your analytical chemist of choice…)
SLIDE 4
Experimental Knowledge
- A lot of effort is made to analyze MS, MS2, MS3 spectra, but…
- Separation dimension or other orthogonal methods are often neglected
- Liquid Chromatography (LC)
- Incl. 2D-LC
- Gas Chromatography (GC)
- Incl. 2D-GC
- Capillary Electrophoresis (CE)
- Supercritical Fluid Chromatography (SFC)
- Ion Mobility Spectrometry (IMS)
- Traveling wave
- FAIMS
- Drift tube
That information has to be also stored somewhere!!! (CV for that!!!)
SLIDE 5
Retention time indexing in (RP-)LC-MS
Michael Quilliam, personal communication
SLIDE 6
Retention time indexing in (RP-)LC-MS
A New Retention Index System for LC-MS, HPLC 2015, Geneva
SLIDE 7
Retention time indexing in (RP-)LC-MS
Spiked to matrix neat
SLIDE 8
Retention time indexing in (RP-)LC-MS
- Evaluation of different matrices
- Plants
- Plasma
- Urine
- C. elegans extracts
- Bacterial extracts
- Feces
- Liver extracts
- Evaluation of different gradients
- Evaluation of different column
dimensions
- Different chemistries and
projection between different systems
- Ring-trial recently started
SLIDE 9
Retention projection/prediction
Jan Stanstrup, Steffen Neumann, and Urška Vrhovšek PredRet: Prediction of Retention Time by Direct Mapping between Multiple Chromatographic Systems
- Anal. Chem., 2015, 87 (18), pp 9421–9428
SLIDE 10
Retention time prediction in metabolomics
SLIDE 11
Data set overview
- Creek et al.
- ZIC-HILIC
- 120 standards
- MLR on 6 descriptors, 35% CV
- Eugster et al.
- BEH C18
- 260 standards
- PLS, ANN on 8 descriptors, 2.5 minutes 30 min gradient CV
- Cao et al.
- ZIC-pHILIC
- 93 standards
- RF, MLR on 11 descriptors, 5.1% error no CV, 9.4% CV
SLIDE 12
Creek et al.
Darren J. Creek, Andris Jankevics, Rainer Breitling, David G. Watson, Michael P. Barrett, and Karl E. V. Burgess Toward Global Metabolomics Analysis with Hydrophilic Interaction Liquid ChromatographyMass Spectrometry: Improved Metabolite Identification by Retention Time Prediction Anal Chem. 2011 Nov 15;83(22):8703-10. doi: 10.1021/ac2021823. Epub 2011 Oct 21.
SLIDE 13
Eugster et al.
Philippe J. Eugster, Julien Boccard, Benjamin Debrus, Lise Bréant, Jean-Luc Wolfender, Sophie Martel, Pierre-Alain Carrupt Retention time prediction for dereplication of natural products (CxHyOz) in LC–MS metabolite profiling
- Phytochemistry. 2014 Dec;108:196-207
SLIDE 14
Cao et al.
C5H11NO3S
Mingshu Cao, Karl Fraser, Jan Huege, Tom Featonby, Susanne Rasmussen, Chris Jones Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics
- Metabolomics. 2015;11(3):696-706. Epub 2014 Sep 7.
SLIDE 15
PC(37:1) [M+H]+ HexCer(d40:3) [M+Na]+ SM(t40:1)/PE-Cer(t43:1) [M+H]+
SLIDE 16