scholarly journals Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

2020 ◽  
Author(s):  
Daniel Petras ◽  
Jeremiah J. Minich ◽  
Lucia B. Cancelada ◽  
Ralph R. Torres ◽  
Emily Kunselman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Organic Matter ◽  
Data Analysis ◽  
Tandem Mass Spectrometry ◽  
Molecular Mapping ◽  
Anthropogenic Impacts ◽  
Marine Ecosystems ◽  
Chemical Pollution ◽  
Rain Event ◽  
Tandem Mass

Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter chemotypes including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after significant rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa(methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.<br>

scholarly journals Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

2020 ◽  
Author(s):  
Daniel Petras ◽  
Jeremiah J. Minich ◽  
Lucia B. Cancelada ◽  
Ralph R. Torres ◽  
Emily Kunselman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Organic Matter ◽  
Data Analysis ◽  
Tandem Mass Spectrometry ◽  
Molecular Mapping ◽  
Anthropogenic Impacts ◽  
Marine Ecosystems ◽  
Chemical Pollution ◽  
Rain Event ◽  
Tandem Mass

Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter chemotypes including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after significant rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa(methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.<br>

Non-target tandem mass spectrometry enables the prioritization of anthropogenic pollutants in seawater along the northern San Diego coast

2019 ◽  
Author(s):  
Daniel Petras ◽  
Jeremiah J. Minich ◽  
Emily Kunselman ◽  
Mingxun Wang ◽  
Margot E. White ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Tandem Mass Spectrometry ◽  
San Diego ◽  
Marine Ecosystems ◽  
Chemical Pollution ◽  
Rain Event ◽  
Tandem Mass ◽  
Molecular Networking ◽  
Anthropogenic Pollutants

Anthropogenic pollutants inundate marine ecosystems as human population growth and urbanization rapidly increase along the coast. The analytical methods applied to detect anthropogenic imprints in coastal seawater are historically aimed at measuring and monitoring a restricted number of compounds. More recently applied non-targeted approaches are typically still limited by spectral and structure library coverage. To prioritize anthropogenic impacts in marine systems beyond compounds present in libraries and suspect lists, we applied non-targeted liquid chromatography tandem mass spectrometry in combination with molecular networking. We integrated an advanced data analysis pipeline that allows scalable comparison of chemotypes between samples in addition to expanded compound annotation using molecular networking. Using this workflow, we explored the chemical impacts of a major rain event in January 2018 in coastal San Diego, USA in a total of 120 samples. We detected 4384 ion features and could annotate 92 MS/MS spectra by spectrum library matching of which 40 annotations were putative xenobiotics. The observed seawater chemotype shifted significantly after the rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, such as pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa(methoxymethyl)melamine). Expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we could further contextualize their possible origin and show their potential importance in other ecosystems. Ultimately, the mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which we hope will contribute to a more deliberate assessment of how chemical pollution impacts marine environments.<br>

Non-Targeted Metabolomics Enables the Prioritization and Tracking of Anthropogenic Pollutants in Coastal Seawater

2019 ◽  
Author(s):  
Daniel Petras ◽  
Jeremiah J. Minich ◽  
Emily Kunselman ◽  
Mingxun Wang ◽  
Margot E. White ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Tandem Mass Spectrometry ◽  
Marine Ecosystems ◽  
Point Sources ◽  
Rain Event ◽  
Tandem Mass ◽  
Analysis Pipeline ◽  
Anthropogenic Pollutants ◽  
Data Analysis Pipeline

Anthropogenic pollutants inundate marine ecosystems as human population growth and urbanization rapidly increase along the coast. Our analytical methods are typically aimed at measuring and monitoring a restricted number of compounds. To prioritize coastal anthropogenic impacts in a comprehensive fashion, we applied large-scale non-targeted liquid chromatography tandem mass spectrometry. We integrated an advanced data analysis pipeline that allows scalable comparison of chemotypes between samples in addition to expanded compound annotation using molecular networking. Using this workflow, we explored the chemical impacts of a major rain event in January 2018 in coastal San Diego, USA. We observed the seawater chemotype shift significantly after the rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, such as pesticides, cleaning products, drugs and chemical additives that could be connected to potential point sources. Expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we could further contextualize their origin and show their potential importance in other ecosystems. Ultimately, the mass spectrometry and data analysis pipeline applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which we hope will contribute to a more deliberate assessment of how chemical pollution impacts marine environments.

scholarly journals Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics

Proteomes ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 15
Author(s):  
Benjamin C. Orsburn
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Tandem Mass Spectrometry ◽  
Data Processing ◽  
Recent History ◽  
Tandem Mass ◽  
Central Theme ◽  
Initial Release ◽  
Proteome Discoverer

Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today.

scholarly journals Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Chemosphere ◽  
2021 ◽  
pp. 129450
Author(s):  
Daniel Petras ◽  
Jeremiah J. Minich ◽  
Lucia B. Cancelada ◽  
Ralph R. Torres ◽  
Emily Kunselman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Organic Matter ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Coastal Seawater
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