Waters Targeted Omics Method Library (TOML) provides instant access to a wide variety of valuable targeted LC-MS/MS methods. Created by some of the world’s best method developers, TOML method packages include an application note for the method, a method file containing all of the chromatographic and spectrometric settings for the method, and a list of stable-isotope labeled standards for the method. By simply downloading and importing the method files, you can expand the menu of assays provided in your lab in a matter of hours. TOML is provided free of charge to further enhance the value of your Waters LC-MS system.
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.
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.
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.
Method Package |
Short Description |
Application Note |
Acylcarnitines-R |
A rapid, targeted RP UPLC-MS/MS method for the measurement of acylcarnitines without the need for derivitization. Simultaneous analysis of 20 acylcarnitines in a single analytical run that is under three minutes. |
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Amino Acids-R |
A rapid, high-throughput RP UPLC-MS/MS research method for the analysis of derivatized amino acids samples for metabolomic research studies. |
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Bile Acids-R |
A rapid, targeted RP UPLC-MS/MS method for the measurement of bile acids for metabolomic research studies. |
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Oxylipins |
A targeted UPLC-MS/MS methodology for the semi-quantitative profiling of bioactive oxylipins (oxidized fatty acids) in plasma/serum and cell culture media. |
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Steroids-R |
A rapid UPLC-MS/MS methodology has been developed for the research analysis of 14 endogenous steroids in human plasma and serum. |
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TCA Cycle Intermediates |
A rapid, targeted non-ion pairing, mixed-mode method for the measurement of TCA cycle intermediates for metabolomic research studies. |
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Tryptophan-R |
A rapid UPLC-MS/MS methodology has been developed for the analysis of tryptophan and seven of its metabolites in various matrices. |
Method Package |
Short Description |
Application Note |
Diacyl Phosphatidylcholines-R |
A rapid, targeted UPLC-MS/MS methodology has been developed for the semi-quantitative analysis of 57 diacyl-phosphatidylcholine species in human serum. |
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Free Fatty Acids-R |
A rapid, targeted RP UPLC-MS/MS method for measurement of free fatty acids for metabolomic research studies, without the need for derivitization. |
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High-Throughput HILIC-MS/MS |
A high-throughput, quantitative, and comprehensive HILIC UPLC-MS/MS method for the analysis of 16 polar and non-polar lipid classes in plasma. |
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Triglycerides-R |
A rapid RP UPLC-MS/MS methodology has been developed for the analysis of triglycerides in biomedical research. |
For Research Use Only. Not for Use in Diagnostic Procedures.** |
The Quanpedia Library file access requires a short form completion.
Kit |
Short Description |
Application Note/Publication |
Biocrates P180 |
A standardized quantitative Kit that allows the simultaneous analysis of more than 180 endogenous metabolites in 10 μL as typical sample volume from five different key metabolite classes. |
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Biocrates MxP Quant 500 |
A standardized quantitative Kit that allows the simultaneous analysis of up to 630 metabolites and lipids from 26 analyte classes in a 10-uL sample. An additional 232 biologically relevant sums and ratios can be calculated. |
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Biocrates Bile Acids |
A standardized quantitative Kit developed that allows the simultaneous analysis of 20 bile acids in 20 μL sample volume. The kit has been validated according to the EMA guidelines for human and rat plasma. |
App Note |
Kairos Amino Acid |
The Kairos Amino Acid Kit is fully automated with manual options for physiological samples in both high-throughput (500+ samples) and lower-throughput (100+ samples) amino acid analysis. Built on AccQ•Tag reaction chemistry, this kit enables retesting of samples a breeze. Run times of under 10 minutes. |
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Biognosys PQ100 PlasmaDive 100 |
A high-throughput RP UPLC-MS/MS research kit for the semi-quantitative analysis of various tryptic peptides in human serum samples. |
What is Quanpedia?
Waters TOML method packages contain Quanpedia method files. Quanpedia is a compound-centric database that holds all UPLC chromatographic, MS/MS acquisition, and data (TargetLynx) quantitation information in one place and is included in Waters MassLynx software. Information contained in Quanpedia may be edited and/or supplemented manually to enable end-user customization.
User's Guide
A comprehensive user’s guide for the LipidQuan Method Package
Video Guides
The following are How-To Videos for downloading TOML method packages, importing and running methods, and data processing:
MetaboQuan
LipidQuan