Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN

Abstract

Neutral loss (NL) spectral data presents a mirror of MS² data and is a valuable yet largely untapped resource for molecular discovery and similarity analysis. Tandem mass spectrometry (MS²) data is effective for the identification of known molecules and the putative identification of novel, previously uncharacterized molecules (unknowns). Yet, MS² data alone is limited in characterizing structurally related molecules. To facilitate unknown identification and complement the METLIN-MS² fragment ion database for characterizing structurally related molecules, we have created a MS² to NL converter as a part of the METLIN platform. The converter has been used to transform METLIN's MS² data into a neutral loss database (METLIN-NL) on over 860 000 individual molecular standards. The platform includes both the MS² to NL converter and a graphical user interface enabling comparative analyses between MS² and NL data. Examples of NL spectral data are shown with oxylipin analogues and two structurally related statin molecules to demonstrate NL spectra and their ability to help characterize structural similarity. Mirroring MS² data to generate NL spectral data offers a unique dimension for chemical and metabolite structure characterization.

Figure 1.

The METLIN-NL mass spectral database was derived from the METLIN-MS² data on over 860,000 molecular standards. (A) Asymmetric dimethylarginine (ADMA) and its representative METLIN-MS² spectra at four different collision energies. (B) METLIN-NL spectra (NL_intensity vs. Δm/z) of ADMA was generated by calculating the difference between the precursor and fragment ions with NL_intensity based on the original fragment ion intensities. “P” refers to precursor ion and “F” refers to fragment ion.

Figure 2.

MS² and NL data on two related oxylipins (16 keto 16-B₁-PhytoP and 16-B₁-PhytoP) and the statin drugs rosuvastatin and desmethyl rosuvastatin. (A) Oxylipin MS² data show little overlap (in red) in contrast to the (B) NL spectra with the high resolution neutral loss data facilitating similarity analysis with both providing complementary structural information. The red box denotes the only (minor) structural differences between the two molecules.

Figure 3.

Synergy between MS² and neutral loss data on two related sphingosine molecules. Dimethyl sphingosine and sphingosine C20 (A) MS² and (B) neutral loss data, both the MS² data and the neutral loss data show both overlapping and distinctly different peaks. The red box denotes the structural differences between the two molecules.

Figure 4.

MS² and NL data on two related statins. Rosuvastatin and desmethyl rosuvastin (A) MS² and (B) NL data, the MS² data show few overlapping peaks (in red) while the NL spectra provide near complete overlap. Interestingly, while the NLs help facilitate similarity, the MS² data provides more structurally distinguishing features. The red box denotes the only (minor) structural differences between the two molecules.