Shot-Gun Lipidomics


Direct infusion was originally used to efficiently deliver lipid samples and to avoid difficulties of lipid analysis from alterations in concentration, chromatographic anomalies, and ion-pairing alterations in early 1990. Around 2004, the platforms developed based on this strategy were separately named as "shotgun lipidomics" by Han and Gross and Ejsing et al. Since then, this technology has become one of the widely used approaches in lipidomics, particularly for high-throughput analysis of lipids.

The most basic device to deliver lipid solution for direct infusion is a syringe pump. This device is relatively low cost and can be constructed to deliver a few microliters of solution per minute. Its major weakness is that automation of lipid analysis is difficult to achieve with this delivery system. Clogging of the delivery capillary line occurs frequently, even if the samples are prepared carefully. Moreover, the requirement of a relatively high flow rate for stabilizing the ion current makes the consumption of a large volume of lipid solution, thus a large amount of source biological materials.
Shot-Gun Lipidomics
Shot-Gun Lipidomics Service
Robotic nanoflow ion sources (e.g., NanoMate device) make the direct infusion automated and eliminates all the aforementioned limitations by using a syringe pump, i.e., substantial reduction of potential sample clogging and dramatic reduction of the sample size and cross-contamination. A major drawback of utilizing this device is its relatively high cost. A major concern of handling small volume lipid samples is the solvent evaporation during long automated analysis.


  • Tandem mass spectrometry-based shotgun lipidomics (Triple quadrupole mass spectrometer)
  • High mass accuracy-based shotgun lipidomics (Q-TOF; Quadrupole-OrbiTrap)
  • Multi-dimensional MS-based shotgun lipidomics

Advantages and Drawbacks

Tandem mass spectrometry-based shotgun lipidomicsSimplicity, efficiency, high sensitivity, ease of management, and less expensive instrumental requirements
  • The fatty acyl substituents of lipid species are not identified since the approach only targets to the class-specific head group fragments
  • The detection with the so-called specific MS/MS scanning might not be entirely specific to the class or the category of classes of interest, whereas this non-specificity might lead to introduction of some artifacts
  • Some altered ionization conditions cannot be easily recognized during and after the experiments
  • Accurate quantification of the detected lipid species might not be s simple as expected because of the differential fragmentation thermodynamics and kinetics manifest in individual lipid species within each lipid class
High mass accuracy-based shotgun lipidomicsThis shotgun lipidomics strategy provides efficient, broad, and sensitive measurement of lipid species in a high-throughput fashion.
  • Since quantification of lipid species in the multi-PIS (NLS) strategy is based on tandem MS techniques, it is better to include multiple (at least two) internal standards for each lipid class to cover the differential fragmentation thermodynamics/kinetics of different molecular species
  • Differential ionization responses of different species among a non-polar lipid class are well known and correction for these differential ionization responses in quantification of these species should be considered
  • Linear dynamic range of quantification largely depends on the used instrument under experimental conditions in either multi-PIS (NLS) or high mass accuracy strategies
  • It might not be the best choice to analyze poorly ionized lipids, particularly those in low abundance through this approach
Multi-dimensional MS-based shotgun lipidomicsThis approach minimizes the ion suppression effects, eliminates the presence of any artifactual species.
MDMS-SL is ideally suited to exploit the distinctive chemical characteristics of many lipid classes.
  • MDMS-SL is relatively low throughput and laborious because of the involvement of different procedures (e.g., derivatization) in multiplexed sample preparation
  • MDMS-SL is unable to distinguish isomeric species
  • Although MDMS-SL identifies and quantifies all individual species of a characterized lipid class in an unbiased fashion within the limits of instrumentation sensitivities, the approach is not ideal for identification and quantitation of species of an unknown or uncharacterized lipid class since identification of the building blocks of a lipid class has to be pre-determined


  1. Wang, Miao.; et al. Novel advances in shotgun lipidomics for biology and medicine. Progress in lipid research. 2016, 61: 83-108.

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