Fig. 1: Overview of the Dynamic Organellar Maps workflow, DIA optimization strategy, and evaluation with DOM-ABC. | Nature Communications

Fig. 1: Overview of the Dynamic Organellar Maps workflow, DIA optimization strategy, and evaluation with DOM-ABC.

From: Deep and fast label-free Dynamic Organellar Mapping

Fig. 1

HeLa cell lysates were fractionated by differential centrifugation, to generate triplicate reference organellar maps. Following tryptic digest, samples were analyzed by LC-MS, using either a Thermo EASY-nLC 1200 HPLC, or a high-throughput Evosep One HPLC, coupled to a Thermo Exploris 480 orbitrap mass spectrometer. Data were acquired in DDA or DIA mode, and DIA processing was performed with library or discovery DIA. For the performance evaluation, data were analyzed with the web app DOM-ABC (https://domabc.bornerlab.org), which provides multiple info graphics and metrics for assessing map topology, proteomic depth, map resolution and reproducibility, as well as differential analysis for detection of translocating proteins and machine learning based localization prediction.

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