A recent commentary by Giera et al. (link) sparked a discussion about in-source fragmentation (ISF). The authors claimed that “ISF could account for over 70% of the peaks observed in typical LC–MS/MS metabolomic datasets”. This claim, echoed by other outlets, even went as far as suggesting that “over 70% of the dark metabolome could be an experimental artefact” (link). Many metabolomics practitioners reacted with…
NOTE: After the initial publication of this post, we added more details and results on the correct (!) annotation of lipids with multiple double bonds. It's at the end. NOTE 2: The annotation workflow with 3rd gen annotation for CID and EAD is ready for external testing. If you are interested, drop me an email. One of the grand challenges in metabolomics using mass…
This year we celebrate the 10th anniversary of one of our QTOFs. It is not among the oldest mass spectrometers that we have in the lab, but it is a special case in many senses. The anniversary evoked both retrospective and prospective reflections, which I wanted to share to hear about the experience of others. The first ten years The birthday boy is an…
This post will describe the journey towards MSNovelist, a project I have been working on over the last two years and which is now finally available as a preprint here. MSNovelist is a de novo structure elucidation method for MS2 spectra. Background De novo indicates that molecular structures are generated directly from the MS2 spectrum without referring to a database. In contrast to existing…
Imagine running a study with 100 samples by untargeted LC-MS (polar or lipids, you pick!). Data acquisition by DIA/DDA in complete in 1-2 days, and comes the step of data analysis. The minimum expectation for the software is to find all peaks across samples (rare and frequent, high and low, symmetric and tailing peaks), take care of shifts in m/z and RT, group isotopologues…
Background For >10 years, we analysed all kinds of samples by flow injection analysis - HRMS. I will not discuss the pros and cons of including a column (LC-MS) or omitting it (FIA-MS). In brief, FIA-MS is great to profile endogenous metabolites from cellular systems, less for the more exotic samples that require in-depth MS2. Believe it or not, we used FIA to profile>1.4…