loading page

Establishing A Comprehensive Workflow for Extracting MS1 Isotope Distributions in LC-MS/MS Proteomics
  • +2
  • Frédérique Vilenne,
  • Annelies Agten,
  • Simon Appeltans,
  • Gökhan Ertaylan,
  • Dirk Valkenborg
Frédérique Vilenne
Hasselt University

Corresponding Author:frederique.vilenne@uhasselt.be

Author Profile
Annelies Agten
Hasselt University
Author Profile
Simon Appeltans
Hasselt University
Author Profile
Gökhan Ertaylan
Flemish Institute for Technological Research
Author Profile
Dirk Valkenborg
Hasselt University
Author Profile


The continuous advancements in LC-MS/MS proteomics over the past decades have paved the way for transformative changes in the field of medicine, particularly in the realms of preventive and personalized healthcare. Many new algorithms are evaluated on unknown proteomes and using databases with annotated MS2-spectra. When the research is focused on MS1-spectra, such databases are not available yet. Specifically, we propose a comprehensive workflow to extract MS1 isotope distributions from spectra, which we validated using a proteomics standard kit comprising known proteins at varying concentrations in duplicate. Our workflow incorporated a database search utilizing a state-of-the-art algorithm at 1% FDR. Through this approach, we investigated the impact of protein concentration on the probability of protein identification. Confidently identified PSMs were used to extract the MS1 isotope distributions through the proposed workflow. A total of 138.111 MS1 isotope distributions were extracted. Isotope distributions with 2 or more peaks were compared with their theoretical isotope distributions using the spectral angle. A median spectral angle of 0,101 and 0,0992 was observed in both samples indicating a high similarity. The findings from this study were compiled into a dataset which can potentially facilitate the development of novel tools with a focus on MS1 data.
31 May 2023Submitted to PROTEOMICS
01 Jun 2023Assigned to Editor
01 Jun 2023Review(s) Completed, Editorial Evaluation Pending
01 Jun 2023Submission Checks Completed
01 Jun 2023Reviewer(s) Assigned
17 Jul 2023Editorial Decision: Revise Minor
01 Sep 2023Review(s) Completed, Editorial Evaluation Pending
01 Sep 20231st Revision Received
04 Sep 2023Reviewer(s) Assigned