Towards a universal LC-MS screening procedure - can an LIT LC-MS(n) screening approach and reference library be used on a quadrupole-LIT hybrid instrument?

J Mass Spectrom. 2012 Jan;47(1):66-71. doi: 10.1002/jms.2027.


In contrast to libraries with highly reproducible gas chromatography electron ionization mass spectra, current liquid chromatography (LC-MS) libraries are limited to specific instrument types. Therefore, the aim of the study was to prove whether a recently developed linear ion trap (LIT) LC-MS(n) screening approach and reference library can be transferred to an LC-MS/MS system with a quadrupole-LIT hybrid mass analyzer using SmileMS, a sophisticated search algorithm. The LIT reference library was built with MS² and MS³ wideband spectra recorded on a ThermoFisher LXQ LIT with electrospray ionization in positive mode and full-scan data-dependent acquisition (DDA). Collision parameter optimizations, including different scan types and energies, were performed on an Applied Biosystems QTRAP 4000 system using electrospray ionization in positive mode and full-scan DDA. Modified library sets were generated to improve the detection of a compound by the used search algorithm. Additionally, 100 authentic human urine samples were screened by both systems for proof of applicability. In the applicability study, 533 compounds were detected by the LXQ and 477 by the QTRAP system using enhanced product ion scan and a modified database. The presented data showed that the LIT screening approach and reference library could be used successfully on a QTRAP instrument with some limitations. These should be overcome by further optimizations regarding DDA settings for better sensitivity and further library modifications to reduce spectra mismatches.

MeSH terms

  • Algorithms
  • Chromatography, Liquid / instrumentation
  • Chromatography, Liquid / methods
  • Chromatography, Liquid / standards*
  • Databases, Factual*
  • Humans
  • Pharmaceutical Preparations / urine
  • Reproducibility of Results
  • Spectrometry, Mass, Electrospray Ionization
  • Statistics, Nonparametric
  • Tandem Mass Spectrometry / instrumentation
  • Tandem Mass Spectrometry / methods
  • Tandem Mass Spectrometry / standards*


  • Pharmaceutical Preparations