Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations

Sanders, Katherine L.; Edwards, John A.

doi:10.1039/d0ay01194k

Cited by 31 publications

(25 citation statements)

References 145 publications

(148 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This fact was established during keyword mining as well as bioconcept co-occurrence networks. The frequent keywords also suggested that the most frequent methodologies are 2D-gel-electrophoresis, mass spectrometry, matrix-assisted laser desorption-ionization, liquid chromatography, computational biology which are the most common ones in the case of proteome and proteomics research [ 32 , 33 , 34 , 35 ].…”

Section: Discussionmentioning

confidence: 99%

Mining Proteome Research Reports: A Bird’s Eye View

Sahu

2021

Proteomes

View full text Add to dashboard Cite

The complexity of data has burgeoned to such an extent that scientists of every realm are encountering the incessant challenge of data management. Modern-day analytical approaches with the help of free source tools and programming languages have facilitated access to the context of the various domains as well as specific works reported. Here, with this article, an attempt has been made to provide a systematic analysis of all the available reports at PubMed on Proteome using text mining. The work is comprised of scientometrics as well as information extraction to provide the publication trends as well as frequent keywords, bioconcepts and most importantly gene–gene co-occurrence network. Out of 33,028 PMIDs collected initially, the segregation of 24,350 articles under 28 Medical Subject Headings (MeSH) was analyzed and plotted. Keyword link network and density visualizations were provided for the top 1000 frequent Mesh keywords. PubTator was used, and 322,026 bioconcepts were able to extracted under 10 classes (such as Gene, Disease, CellLine, etc.). Co-occurrence networks were constructed for PMID-bioconcept as well as bioconcept–bioconcept associations. Further, for creation of subnetwork with respect to gene–gene co-occurrence, a total of 11,100 unique genes participated with mTOR and AKT showing the highest (64) number of connections. The gene p53 was the most popular one in the network in accordance with both the degree and weighted degree centrality, which were 425 and 1414, respectively. The present piece of study is an amalgam of bibliometrics and scientific data mining methods looking deeper into the whole scale analysis of available literature on proteome.

show abstract

Section: Discussionmentioning

confidence: 99%

Mining Proteome Research Reports: A Bird’s Eye View

Sahu

2021

Proteomes

View full text Add to dashboard Cite

show abstract

“…For instance, back in 2008, EVs proteomic analysis in C. neoformans led to identification of 76 proteins ( Rodrigues et al, 2008 ). Current high-resolution tandem mass spectrometry (HR-MS/MS)-based approaches ( Lesur and Domon, 2015 ), including nanoflow liquid chromatography coupled to HR-MS/MS (nanoLC-HR-MS/MS; Sanders and Edwards, 2020 ), allow to identify and quantify over 2,000 proteins in fungal EVs ( Zhao et al, 2019 ; Cleare et al, 2020 ). In this section, we will cover recent technological advances and their current impact and perspectives in analyzing fungal EVs.…”

Section: New Methodologies and Instrumentationmentioning

confidence: 99%

Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles

et al. 2021

View full text Add to dashboard Cite

Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all kingdoms of life. The diverse biogenesis pathways of EVs result in a wide variety of physical properties and functions across different organisms. Fungal EVs were first described in 2007 and different omics approaches have been fundamental to understand their composition, biogenesis, and function. In this review, we discuss the role of omics in elucidating fungal EVs biology. Transcriptomics, proteomics, metabolomics, and lipidomics have each enabled the molecular characterization of fungal EVs, providing evidence that these structures serve a wide array of functions, ranging from key carriers of cell wall biosynthetic machinery to virulence factors. Omics in combination with genetic approaches have been instrumental in determining both biogenesis and cargo loading into EVs. We also discuss how omics technologies are being employed to elucidate the role of EVs in antifungal resistance, disease biomarkers, and their potential use as vaccines. Finally, we review recent advances in analytical technology and multi-omic integration tools, which will help to address key knowledge gaps in EVs biology and translate basic research information into urgently needed clinical applications such as diagnostics, and immuno- and chemotherapies to fungal infections.

show abstract

“…A comprehensive summary of theory, common approaches, and over 20 of the most recent applications of nano-LC-MS in metabolomics and lipidomics investigation can be found elsewhere. 232 Single cell analysis is an emerging application of small-scale metabolomics by nano-LC-MS. Recently, Nakatani et al reported a method for derivatization-free targeted quantification of hydrophilic metabolites in single HeLa cells.…”

Section: Navigating the Conflicting Goals Of Metabolome Coverage And mentioning

confidence: 99%

“…In such cases, the full sensitivity potential of nano-RP-LC-MS platforms may be exploited by analyte derivatization, increasing RP-retention and ionization efficiency. A comprehensive summary of theory, common approaches, and over 20 of the most recent applications of nano-LC-MS in metabolomics and lipidomics investigation can be found elsewhere . Single cell analysis is an emerging application of small-scale metabolomics by nano-LC-MS.…”

Section: Navigating the Conflicting Goals Of Metabolome Coverage And ...mentioning

confidence: 99%

Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics—Standardization, Coverage, and Throughput

et al. 2020

View full text Add to dashboard Cite

Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations

Abstract: Liquid chromatography coupled to mass spectrometry (LC-MS) is one of the most powerful tools in identifying and quantitating molecular species. Decreasing column diameter from the millimeter to micrometer scale is...

Cited by 31 publications

References 145 publications

Mining Proteome Research Reports: A Bird’s Eye View

Mining Proteome Research Reports: A Bird’s Eye View

Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles

Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics—Standardization, Coverage, and Throughput

Contact Info

Product

Resources

About