Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation SummaryLipidMS was initially envisioned to use fragmentation rules and data-independent acquisition (DIA) for lipid annotation. However, data-dependent acquisition (DDA) remains the most widespread acquisition mode for untargeted LC-MS/MS-based lipidomics. Here we present LipidMS 3.0, an R package that not only adds DDA and new lipid classes to its pipeline, but also the required functionalities to cover the whole data analysis workflow from pre-processing (i.e., peak-peaking, alignment and grouping) to lipid annotation. We applied the new workflow in the analysis of a serum dataset acquired in MS, DDA and DIA modes. Our results show that LipidMS 3.0 data pre-processing outperforms XCMS and complements those lipids annotated using MS-DIAL, one of the most widely used tools in lipidomics. To extend and facilitate LipidMS 3.0 usage among less experienced R-programming users the workflow has been also implemented as a web-based application.

Availability and ImplementationLipidMS R-package is freely available at https://CRAN.R-project.org/package=LipidMS and as a website at http://www.lipidms.com.
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The categories of this paper are: microbiology
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The categories of this paper are: pharmacology
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The categories of this paper are: evolutionary
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The categories of this paper are: education
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The categories of this paper are: and
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The categories of this paper are: biophysics
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The categories of this paper are: developmental
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The categories of this paper are: toxicology
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The categories of this paper are: neuroscience
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The categories of this paper are: biology
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The categories of this paper are: communication
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The categories of this paper are: molecular
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The categories of this paper are: synthetic
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The categories of this paper are: cancer
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The categories of this paper are: epidemiology
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The categories of this paper are: scientific