Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics

Anal Chem. 2017 Jul 5;89(13):7046-7052. doi: 10.1021/acs.analchem.7b00794. Epub 2017 Jun 15.


Shotgun lipidomics relies on the direct infusion of total lipid extracts into a high resolution tandem mass spectrometer. A single shotgun analysis produces several hundred of densely populated FT MS and FT MS/MS spectra, each of which might comprise thousands of peaks although a very small percentage of those belong to lipids. Eliminating noise by adjusting a minimal peak intensity threshold is biased and inefficient since lipid species and classes vary in their natural abundance and ionization capacity. We developed a method of peak intensity-independent noise filtering in shotgun FT MS and FT MS/MS spectra that capitalizes on a stable composition of the infused analyte leading to consistent time-independent detection of its bona fide components. Repetition rate filtering relies on a single quantitative measure of peaks detection reproducibility irrespectively of their absolute intensities, masses, or assumed elemental compositions. In comparative experiments, it removed more than 95% of signals detectable in shotgun spectra without compromising the accuracy and scope of lipid identification and quantification. It also accelerated spectra processing by 15-fold and increased the number of simultaneously processed spectra by ∼500-fold hence eliminating the major bottleneck in high-throughput bottom-up shotgun lipidomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Lipids / analysis*
  • Sensitivity and Specificity
  • Tandem Mass Spectrometry / methods*


  • Lipids