Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: case study using a whole cell digest of Clostridium thermocellum

Proteomics
Peter McQueenOleg V Krokhin

Abstract

We have developed a real-time graphic-processor-unit-based search engine capable of high-quality peptide identifications in <500 μs per spectrum. The steps of peptide/protein identification, in-silico prediction of all possible tryptic peptides from these proteins, and the prediction of their expected retention times and m/z values take less than 5 s per cycle over ∼3000 MS/MS spectra. This lays the foundation for information-dependent acquisition with exclusion lists generated on-the-fly, as the instrument continues to acquire data. While a complete evaluation of the dynamic exclusion system requires the participation from instrument vendors, we conducted a series of model experiments using a whole cell tryptic digestion of the bacterium Clostridium thermocellum. We ran a series of five iterative LC-MS/MS runs, adding a new exclusion list at each of four chromatographic "tripping points" - the elution times of the four standard peptides spiked into the sample. Retention times of these standard peptides were also used for real-time "chromatographic calibration." The dynamic exclusion approach gave a ≈ 5% increase in confident protein identification (for typical 2 h LC-MS/MS run), and reduced the average number of identified pep...Continue Reading

References

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Citations

Jun 2, 2014·American Journal of Orthodontics and Dentofacial Orthopedics : Official Publication of the American Association of Orthodontists, Its Constituent Societies, and the American Board of Orthodontics·Wellington J RodyOleg Krokhin
Jan 23, 2016·Mass Spectrometry Reviews·Luminita Moruz, Lukas Käll
Mar 19, 2013·Journal of Proteomics·Kelly HodgeAngus I Lamond
Jul 2, 2019·PLoS Computational Biology·Albert Tian ChenNikolai Slavov
Sep 6, 2018·Extremophiles : Life Under Extreme Conditions·Scott WushkeRichard Sparling
Jun 9, 2020·Journal of the American Society for Mass Spectrometry·Alexander R PelletierMathieu Lavallée-Adam

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