The Targeted Omics Method Library (TOML) Method Packages listed below are available for download. Their access requires a short form completion for regulatory purposes. Once submitted, check your inbox for an email with links to all available files. If you are looking for solutions including kits, please see the “Related Kits” section below.
Targeted Proteomics Method for SARS-CoV-2 Virus Peptides
A recent publication by Conor Jenkins and Benjamin Orsburn, “In Silico Approach to Accelerate the Development of Mass Spectrometry-Based Proteomics Methods for Detection of Viral Proteins", demonstrated the feasibility of an in silico approach to develop LC-MS screening assays for SARS-CoV-2 virus peptides; SARS-CoV-2 causes COVID-19 disease. Restricted access to COVID-19 infected human tissues makes method development challenging. An in silico approach provides a good alternate starting point for targeted proteomics investigation involving SARS-CoV-2 virus. To help accelerate research in better characterizing COVID-19, Waters has generated Quanpedia and Skyline files for theoretical peptides of the virus and have made them available here.
Targeted Proteomics and Lipidomic Methods for SARS-CoV-2 Patient Stratification
A multi-omics paper on “Proteomic and Metabolomic Characterization of COVID-19 Patient Sera” by Bo Shen and co-workers demonstrated that a set of differentially regulated proteins and lipid markers found in patient sera, can be used for the stratification of patients into non-severe and severe categories. Such a stratification is critical to determine the effective treatment plan and optimal use of hospital resources (i.e., ventilators). To expedite your research in understanding COVID-19, the Waters team has developed targeted lipidomics (Quanpedia) and proteomics (Skyline) method packages for the markers used in this paper for the stratification of patients and have made them available here.
Suggested Guidelines for Method Implementation
The proteomics method and associated files were generated in silico using theoretical tryptic peptides MRMs for the SARS-CoV-2 virus. In-laboratory testing and optimization have not been feasible due to limited access to virus infected material. Full implementation of the method should incorporate a chromatographic method using a 1-mm column and a 30-min gradient to separate and quantify the peptides. The provided Skyline file should be used as a starting point to further optimize the conditions, check the peptides and transitions, the collision energy, and the retention times using biological sample. Following complete method optimization, the LC and MS methods can be imported into Quanpedia to streamline the generation of MassLynx acquisition and TargetLynx processing methods.
