Deconvolution for LC-ESI-MS/MS

SpectralWorks Technical Note

SpectralWorks Ltd, United Kingdom

First Published: ASMS 2018.


Electrospray Ionisation (ESI), the preferred technique when using LC-MS is a “soft ionisation” method.  Ideally, very little fragmentation of the molecule occurs leading to a strong pseudomolecular ion. However, adduct formation occurs in the source when a precursor ion interacts with an external atom or molecule to produce an overall charged ion with a known mass difference to the pseudomolecular ion. Isotopes will also be seen and can be distinctive in their ratio to the pseudomolecular ion and allow further interrogation in identification (see table 3).


Optimization of the electrospray voltage for metabolomics samples should focus on applying enough energy to ionize the greatest number of the molecules but not so high as to cause further fragmentation. This is the “middle ground”, where some molecules produce a single pseudomolecular ion (+ adducts and isotopes) and a portion produce multiple ions, more similar to a spectrum produced by GC-EI-MS techniques. It is important to iden#fy which ions are generated from a single molecule 6 355.2743 2.9 m/z 353.2688 isotope 7 497.3109 47.2 [M+H-H2O]+ 8 498.314 14.0 m/z 497.3109 isotope techniques. It is important to identify which ions are generated from a single molecule to reduce any bias introduced when modelling complex data.


Two week old wheat seedlings from different cultivars were prepared for LC-MS analysis by a simple methanol extraction. They were analysed on a Thermo Q-Exac#ve Orbitrap with full scan (for exploratory analysis) and data dependant MS2 (for identification) acquisitions in positive ion mode using a C18 column. The data matrices and chromatographic deconvolution were completed using AnalyzerPro with accurate mass settings and peak detection parameters in figure 1.


Electrospray ionisation can form known and unknown ion patterns during instrumental analyses. Isotopes and known adducts can be monitored for and help in compound identification. However when further fragmentation occurs, these additional masses need to be recognised as a single component.


Catherine Rawlinson, Curtin University, Perth, Western Australia.