Instrument Logic Increases Identifications during Mutliplexed Translatome Measurements

Anal Chem. 2020 Jun 16;92(12):8041-8045. doi: 10.1021/acs.analchem.0c01749. Epub 2020 May 29.


Pulsed Stable Isotope Labeling in Cell culture (SILAC) approaches allow measurement of protein dynamics, including protein translation and degradation. However, its use for quantifying acute changes has been limited due to low labeled peptide stoichiometry. Here, we describe the use of instrument logic to select peaks of interest via targeted mass differences (TMD) for overcoming this limitation. Comparing peptides artificially mixed at low heavy-to-light stoichiometry measured using standard data dependent acquisition with or without TMD revealed 2-3-fold increases in identification without significant loss in quantification precision for both MS2 and MS3 methods. Our benchmarked method approach increased throughput by reducing the necessary machine time. We anticipate that all pulsed SILAC measurements, combined with tandem mass tagging (TMT) or not, would greatly benefit from instrument logic based approaches.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • HeLa Cells
  • Humans
  • Isotope Labeling*
  • Mass Spectrometry
  • Neoplasm Proteins / analysis*
  • Neoplasm Proteins / metabolism
  • Tumor Cells, Cultured


  • Neoplasm Proteins