High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe [article]

Vadim Demichev, Fengchao Yu, Guo Ci Teo, Lukasz Szyrwiel, George Rosenberger, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S. Lilley, Michael Muelleder, Alexey I. Nesvizhskii, Markus Ralser
<span title="2021-03-09">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The dia-PASEF technology exploits ion mobility separation for high-sensitivity analysis of complex proteomes. Here, we demonstrate neural network-based processing of the ion mobility data, which we implement in the DIA-NN software suite. Using spectral libraries generated with the MSFragger-based FragPipe computational platform, the DIA-NN analysis of dia-PASEF raw data increases the proteomic depth by up to 69% compared to the originally published dia-PASEF workflow. For example, we quantify
more &raquo; ... er 5200 proteins from 10ng of HeLa peptides separated with a 95-minute nanoflow gradient, and over 5000 proteins from 200ng using a 4.8-minute separation with an Evosep One system. In complex samples, featuring a mix of human and yeast lysates, the workflow detects over 11700 proteins in single runs acquired with a 100-minute nanoflow gradient, while demonstrating quantitative precision. Hence, the combination of FragPipe and DIA-NN provides a simple-to-use software platform for dia-PASEF data analysis, yielding significant gains in high-sensitivity proteomics.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.03.08.434385">doi:10.1101/2021.03.08.434385</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/frbx6yifczcwlmkkuw34ty2zza">fatcat:frbx6yifczcwlmkkuw34ty2zza</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210310135448/https://www.biorxiv.org/content/biorxiv/early/2021/03/09/2021.03.08.434385.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/a3/f5a30cfcc7c2749ddb76249c75d5eb4f28e20d74.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.03.08.434385"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>