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bioRxiv · 10.1101/681429

The future of peptide-centric Data-Independent Acquisition is predicted

Van Puyvelde, B.·Willems, S.·Gabriels, R.·Daled, S.·De Clerck, L.·Staes, A.·Impens, F.·Deforce, D.·Martens, L.·Degroeve, S.·Dhaenens, M.
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Abstract

Data-Independent Acquisition (DIA) generates comprehensive yet complex mass spectrometric data, which imposes the use of data-dependent acquisition (DDA) libraries for deep peptide-centric detection. We here show that DIA can be redeemed from this dependency by combining predicted fragment intensities and retention times with narrow window DIA. This eliminates variation in library building and omits stochastic sampling, finally making the DIA workflow fully deterministic. Especially for clinical proteomics, this has the potential to facilitate inter-laboratory comparison. Significance of the StudyData-independent acquisition (DIA) is quickly developing into the most comprehensive strategy to analyse a sample on a mass spectrometer. Correspondingly, a wave of data analysis strategies has followed suit, improving the yield from DIA experiments with each iteration. As a result, a worldwide wave of investments in DIA is already taking place in anticipation of clinical applications. Yet, there is considerable confusion about the most useful and efficient way to handle DIA data, given the plethora of possible approaches with little regard for compatibility and complementarity. In our manuscript, we outline the currently available peptide-centric DIA data analysis strategies in a unified graphic called the DIAmond DIAgram. This leads us to an innovative and easily adoptable approach based on predicted spectral information. Most importantly, our contribution removes what is arguably the biggest bottleneck in the field: the current need for Data Dependent Acquisition (DDA) prior to DIA analysis. Fractionation, stochastic data acquisition, processing and identification all introduce bias in the library. By generating libraries through data independent, i.e. deterministic acquisition, stochastic sampling in the DIA workflow is now fully omitted. This is a crucial step towards increased standardization. Additionally, our results demonstrate that a proteome-wide predicted spectral library can surrogate an exhaustive DDA Pan-Human library that was built based on 331 prior DDA runs.

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Van Puyvelde, B., Willems, S., Gabriels, R., Daled, S., De Clerck, L., Staes, A., Impens, F., Deforce, D., Martens, L., Degroeve, S., Dhaenens, M.. 2019-06-26. The future of peptide-centric Data-Independent Acquisition is predicted. https://doi.org/10.1101/681429

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