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 Direct Flavonoid-Focused Chemical Comparison among Three Epimedium Plants by Online Liquid Extraction–High Performance Liquid Chromatography–Tandem Mass Spectrometry

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1520
Author(s):  
Xia Xu ◽  
Ting Li ◽  
Ke Zhang ◽  
Yan Cao ◽  
Li Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
Data Processing ◽  
High Performance ◽  
Liquid Extraction ◽  
Tandem Mass ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass

It is usually a tedious task to profile the chemical composition of a given herbal medicine (HM) using high performance liquid chromatography–tandem mass spectrometry (LC–MS/MS) due to the time-consuming sample preparation and laborious post-acquisition data processing procedures. Even worse, some labile compounds may face degradation risks when exposed to organic solvents for a relatively long period. As one of the most popular HMs, the promising therapeutic benefits of Epimedii Herba (Chinese name: Yinyanghuo) are well defined; however, the chemical profile, and in particular those flavonoids that have been claimed to be responsible for the efficacy, remains largely unknown. Attempts are devoted here to achieve direct LC–MS measurement and efficient post-acquisition data processing, and chemome comparison among three original sources of Epimedii Herba, such as Epimedium sagittatum (Esa), E. pubescens (Epu), and E. koreanum (Eko) was employed to illustrate the strategy utility. A home-made online liquid extraction (OLE) module was introduced at the front of the analytical column to comprehensively transfer the compounds from raw materials onto the LC–MS instrument. A mass defect filtering approach was programmed to efficiently mine the massive LC–MS dataset after which a miniature database was built involving all chemical information of flavonoids from the genus Epimedium to draw a pentagonal frame to rapidly capture potential quasi-molecular ions (mainly [M–H]−). A total of 99 flavonoids (66 in Esa, 84 in Eko, and 66 in Epu) were captured, and structurally annotated by summarizing the mass fragmentation pathways from the mass spectrometric data of authentic compounds and an in-house data library as well. Noteworthily, neutral loss of 144 Da was firstly assigned to the neutral cleavage of rhamnosyl residues. Significant species-differences didn’t occur among their chemical patterns. The current study proposed a robust strategy enabling rapid chemical profiling of, but not limited to, HMs.

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>

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics

PROTEOMICS ◽  
2004 ◽  
Vol 4 (7) ◽  
pp. 1977-1984 ◽  
Author(s):  
Jacques Colinge ◽  
Alexandre Masselot ◽  
Isabelle Cusin ◽  
Eve Mahé ◽  
Anne Niknejad ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Data Processing ◽  
High Performance ◽  
Peptide Identification ◽  
Automatic Data Processing ◽  
Tandem Mass ◽  
Automatic Data

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-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.

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