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Vadim Petrovich Demichev, Łukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda, Daniela Ludwig, Jens Decker, Stephanie Kaspar‐Schoenefeld, Kathryn Susan Lilley and 3 more
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity in proteomic experiments. Here we present a two-dimensional peak-picking algorithm and generation of optimized spectral libraries, as well as take advantage of neural network-based processing of dia-PASEF data. Our computational platform boosts proteomic depth by up to 83% compared to previous work, and is specifically beneficial for fast proteomic experiments and those with low sample amounts. It quantifies over 5300 proteins in single injections recorded at 200 samples per day throughput using Evosep One chromatography system on a timsTOF Pro mass spectrometer and almost 9000 proteins in single injections recorded with a 93-min nanoflow gradient on timsTOF Pro 2, from 200 ng of HeLa peptides. A user-friendly implementation is provided through the incorporation of the algorithms in the DIA-NN software and by the FragPipe workflow for spectral library generation.
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Demichev, V. P., Szyrwiel, Ł., Yu, F., Teo, G. C., Rosenberger, G., Niewienda, A., Ludwig, D., Decker, J., Kaspar‐Schoenefeld, S., Lilley, K. S., Mülleder, M., Nesvizhskii, A. I., & Ralser, M. (2022). dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nature Communications, 13(1), 3944. https://doi.org/10.1038/s41467-022-31492-0
Demichev, Vadim Petrovich, et al. "dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts." Nature Communications, vol. 13, no. 1, 2022, pp. 3944, https://doi.org/10.1038/s41467-022-31492-0.
Demichev, Vadim Petrovich, Łukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda, Daniela Ludwig, et al. "dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts." Nature Communications 13, no. 1 (2022): 3944. https://doi.org/10.1038/s41467-022-31492-0.
Demichev V. P., Szyrwiel Ł., Yu F. [и др.] dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts // Nature Communications. — 2022. — Vol. 13, № 1. — P. 3944. — URL: https://doi.org/10.1038/s41467-022-31492-0
@article{demichev2022diapasef,
title = {{dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts}},
author = {Vadim Petrovich Demichev and Łukasz Szyrwiel and Fengchao Yu and Guo Ci Teo and George Rosenberger and Agathe Niewienda and Daniela Ludwig and Jens Decker and Stephanie Kaspar‐Schoenefeld and Kathryn Susan Lilley and Michael Mülleder and Alexey I. Nesvizhskii and Markus Ralser},
journal = {Nature Communications},
year = {2022},
volume = {13},
number = {1},
pages = {3944},
doi = {10.1038/s41467-022-31492-0},
url = {https://doi.org/10.1038/s41467-022-31492-0}
}TY - JOUR AU - Demichev, Vadim Petrovich AU - Szyrwiel, Łukasz AU - Yu, Fengchao AU - Teo, Guo Ci AU - Rosenberger, George AU - Niewienda, Agathe AU - Ludwig, Daniela AU - Decker, Jens AU - Kaspar‐Schoenefeld, Stephanie AU - Lilley, Kathryn Susan AU - Mülleder, Michael AU - Nesvizhskii, Alexey I. AU - Ralser, Markus TI - dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts JO - Nature Communications VL - 13 IS - 1 SP - 3944 PY - 2022 DA - 2022/07/08 DO - 10.1038/s41467-022-31492-0 UR - https://doi.org/10.1038/s41467-022-31492-0 ER -
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