SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions

Abstract

Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics.

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

“…The metabolomics and lipidomics LC-MS data sets were collected as part of the analyses performed for the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC, https://proteomics.cancer.gov/ programs/cptac) with a 40 min C18 LC separation for lipidomics 19 and a 10 min HILIC LC separation for metabolomics and coupled to a Thermo Lumos mass spectrometer operated with negative ESI (electrospray ionization) and in DDA mode for tandem MS. The metabolomics direct infusion MS data set corresponds to a plant experiment from a modified version of a previously published platform 20 using a Thermo QExactive mass spectrometer operated with negative ESI. The metabolomics LC-IMS-MS and proteomics LC-MS data sets are part of a previous publication of an Agile BioFoundry (http://agilebiofoundry.org) synthetic biology study, 21 with a 10 min HILIC LC separation for metabolomics, coupled to an Agilent 6560 Drift Tube IMS-QTOF mass spectrometer operated with negative ESI and in All Ions DIA mode, and the PNNL-PreProcessor used for data preprocessing, 22 and a 120 min RP LC separation for proteomics, coupled to a Thermo QExactive mass spectrometer operated with positive ESI and DDA mode.…”