1. FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts.
- Author
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Jeong, Kyowon, Babović, Maša, Gorshkov, Vladimir, Kim, Jihyung, Jensen, Ole N., and Kohlbacher, Oliver
- Subjects
ACQUISITION of data ,PROTEOMICS ,CHEMICAL adducts ,POST-translational modification ,ESCHERICHIA coli ,FECAL contamination ,ADOPTED children - Abstract
The detailed analysis and structural characterization of proteoforms by top-down proteomics (TDP) has gained a lot of interest in biomedical research. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complexity of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. Here, we present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In an analysis of E. coli lysate, FLASHIda increases the number of unique proteoform level identifications from 800 to 1500 or generates a near-identical number of identifications in one third of the instrument time when compared to standard DDA mode. Furthermore, FLASHIda enables sensitive mapping of post-translational modifications and detection of chemical adducts. As a software extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates. Data acquisition suitable for top-down proteomics (TDP) has the potential to significantly improve proteoform analysis. Here, the authors present FLASHIda, an intelligent online data acquisition algorithm for TDP that nearly doubles the number of proteoform-level identifications in complex samples. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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