Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset

Analytical Chemistry
Lény GarciaJérôme Lemoine

Abstract

Thanks to comprehensive and unbiased sampling of all precursor ions, the interest to move toward bottom-up proteomic with data-independent acquisition (DIA) is continuously growing. DIA offers precision and reproducibility performances comparable to true targeted methods but has the advantage of enabling retrospective data testing with the hypothetical presence of new proteins of interest. Nonetheless, the chimeric nature of DIA MS/MS spectra inherent to concomitant transmission of a multiplicity of precursor ions makes the confident identification of peptides often challenging, even with spectral library-based extraction strategy. The introduction of specificity at the fragmentation step upon ultraviolet or visible laser-induced dissociation (LID) range targeting only the subset of cysteine-containing peptides (Cys-peptide) has been proposed as an option to streamline and reduce the search space. Here, we describe the first coupling between DIA and visible LID at 473 nm to test for the presence of Cys-peptides with a peptide-centric approach. As a test run, a spectral library was built for a pool of Cys-synthetic peptides used as surrogates of human kinases (1 peptide per protein). By extracting ion chromatograms of query stan...Continue Reading

References

May 19, 2007·Journal of Mass Spectrometry : JMS·Laure JolyJérôme Lemoine
Aug 4, 2011·Physical Chemistry Chemical Physics : PCCP·Rodolphe Antoine, Philippe Dugourd
Jan 18, 2013·Analytical and Bioanalytical Chemistry·Quentin EnjalbertJérôme Lemoine
Oct 22, 2013·Expert Review of Molecular Diagnostics·Yansheng LiuRuedi Aebersold
Aug 26, 2014·Nature Methods·Jonathan D WorboysClaus Jørgensen
Nov 8, 2014·Mass Spectrometry Reviews·Yongsheng Xiao, Yinsheng Wang
Feb 6, 2015·Molecular Systems Biology·Yansheng LiuRuedi Aebersold
Jan 1, 2014·Scientific Data·George RosenbergerRuedi Aebersold
Dec 8, 2016·Nucleic Acids Research·Eric W DeutschJuan Antonio Vizcaíno
Sep 9, 2017·Rapid Communications in Mass Spectrometry : RCM·Lény GarciaMarion Girod

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Citations

Apr 25, 2018·Rapid Communications in Mass Spectrometry : RCM·Marion Girod
Oct 6, 2020·Expert Review of Proteomics·Rui VitorinoFrancisco Amado
Dec 19, 2019·Chemical Reviews·Jennifer S BrodbeltInês Santos
Nov 2, 2019·Analytical Chemistry·Luis A MaciasJennifer S Brodbelt

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