Mass spectrometry session

Summary Fiehn (1)

• Standardization important• Reporting important, but has to be feasible• Does not matter which MS instrument you use, this depends on

the application• Databases are important• Validation is important, al least for known compounds

• Detect identify and quantify all the expected metabolites• Detect, identify (and relative quantification) of the

unexpected metabolites• Metabolome is complex• Dynamic range is very large and can not be covered by any MS

Summary Fiehn: GC-MS

• GC-MS• Problems in GC-MS: injection, film thickness, overloading,

MSTFA differences, differences between instruments, day to day differences

• Quality control is important: standards, quality control samples, Rt index

• Deconvolution, BinBase• GCxGC TOF: academic, suitable for identification, but not

high throughput

LC-MS

• Ion suppression• Coverage of LC-MS: HILIC, CE, RP-HPLC, normal phase, ion

pair• Ionization efficiency• EI vs APCI vs ESI• Absence of large databases with spectra

Minimum control for Quality Control in Targeted Analysis (Newman)

• Validation vs performance characterisation of used methods• Validated robust performance based method• Inappropriate surrogate spiking procedures

• Spike before procedure• Beware of impurities in surrogates• They should correct for analytical variance

• Ongoing assessment of method performance• Minimum calibration requirements• Discrepancies in concentrations of sold calibrants

Improving metabolomics data (Verheij)

• Batch offset• Standardised analysis scheme• Run QC samples, use them as external calibrants• Use more IS select the most suitable for each (also unknown)

analyte

Discussion

• If a target list, what is a target list• Do we need reference material? • Yes we do but we can not wait, so in the meantime we need to

take as many measures as needed to ensure the quality of the data

• We should exchange standards• Start with lists of available standards• Evaluate what you could see on your own platform• Exchange if interested

• Can we compare concentrations from different studies (only doable for known target compounds)

• Exchange columns to check influence on platform performance?

Discussion

• What kind information is necessary to confirm that a feature is actually a compound (MS/MS? Experiments in D2O)

• Can we at least exchange spectra and information on unknowns?

• Who is willing to setup a library• We need LC-MS/MS library• Can we start making claims from different sides (Road map

grant necessary)• Bruce, Oliver and John are going to draft a letter

• Can we at least exchange spectra and information on unknowns?

• Can you take RSDs of analytes into consideration in statistics