Daniel Petras
University of California, San Diego
Mass spectrometryVenomXanthomonas albilineansBiochemistryBiology
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Publications 57
#1Allegra T. Aron (UM: University of Montana)H-Index: 1
#2Emily C. Gentry (UM: University of Montana)H-Index: 1
Last. Fernando Vargas (UM: University of Montana)H-Index: 5
view all 42 authors...
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repositor...
3 CitationsSource
#2Ivan Laponogov (Imperial College London)H-Index: 7
Last. Rachel J. DuttonH-Index: 20
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Gas chromatography-mass spectrometry (GC-MS) represents an analytical technique with significant practical societal impact. Spectral deconvolution is an essential step for interpreting GC-MS data. No public GC-MS repositories that also enable repository-scale analysis exist, in part because deconvolution requires significant user input. We therefore engineered a scalable machine learning workflow for the Global Natural Product Social Molecular Networking (GNPS) analysis platform to enable the ma...
#1Mingxun Wang (UM: University of Montana)H-Index: 16
#2Alan K. Jarmusch (UM: University of Montana)H-Index: 18
Last. Pieter C. DorresteinH-Index: 65
view all 36 authors...
11 CitationsSource
#1Julia M. Gauglitz (UM: University of Montana)H-Index: 8
#2Christine M. Aceves (UM: University of Montana)H-Index: 1
Last. Pieter C. Dorrestein (UM: University of Montana)H-Index: 65
view all 47 authors...
Abstract In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparati...
4 CitationsSource
#1Nicholas R. Casewell (LSTM: Liverpool School of Tropical Medicine)H-Index: 23
#2Daniel Petras (Technical University of Berlin)H-Index: 16
Last. Samuel T. Turvey (ZSL: Zoological Society of London)H-Index: 24
view all 33 authors...
Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents th...
1 CitationsSource
#1Carsten Simon (MPG: Max Planck Society)H-Index: 1
#2Tania P. PimentelH-Index: 7
Last. Gerd Gleixner (MPG: Max Planck Society)H-Index: 57
view all 11 authors...
#1Marcus Ludwig (FSU: University of Jena)H-Index: 2
#2Louis-Felix Nothias (UCSD: University of California, San Diego)H-Index: 13
Last. Sebastian Böcker (FSU: University of Jena)H-Index: 33
view all 12 authors...
The confident high-throughput identification of small molecules remains one of the most challenging tasks in mass spectrometry-based metabolomics. SIRIUS has become a powerful tool for the interpretation of tandem mass spectra, and shows outstanding performance for identifying the molecular formula of a query compound, being the first step of structure identification. Nevertheless, the identification of both molecular formulas for large compounds above 500 Daltons and novel molecular formulas re...
3 CitationsSource
#1Louis-Felix Nothias (UCSD: University of California, San Diego)H-Index: 13
#2Daniel Petras (UCSD: University of California, San Diego)H-Index: 16
Last. Pieter C. Dorrestein (UCSD: University of California, San Diego)H-Index: 65
view all 62 authors...
Molecular networking has become a key method used to visualize and annotate the chemical space in non-targeted mass spectrometry-based experiments. However, distinguishing isomeric compounds and quantitative interpretation are currently limited. Therefore, we created Feature-based Molecular Networking (FBMN) as a new analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure. FBMN leverages feature detection and alignment tools to enhance quantitative analys...
8 CitationsSource
#1Sabah Ul-Hasan (UCM: University of California, Merced)H-Index: 3
#2E. Rodríguez-Román (IVIC: Venezuelan Institute for Scientific Research)H-Index: 2
Last. Timothy J. Colston (FSU: Florida State University)H-Index: 7
view all 14 authors...
Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, endoparasites, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to dat...
1 CitationsSource
#1Evan Bolyen (NAU: Northern Arizona University)H-Index: 8
#2Jai Ram Rideout (NAU: Northern Arizona University)H-Index: 13
Last. J. Gregory Caporaso (NAU: Northern Arizona University)H-Index: 48
view all 112 authors...
In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited H...
3 CitationsSource