SWATH to MRM Builder App

Transcription

1 SWATH to MRM Builder App OneOmics Project RUO-MKT A

2 OneOmics Project Workflow Overview Proteomics Facility Samples SWATH-MS Spectral Reference Libraries Protein Expression Workflow Analytics *.wiff *.wiff *.q res Experiment Manager *.wiff *.wiff *.q res *.q res *.fca Assembler *.wiff *.wiff *.q res Researchers CloudConnect With AutoUpload Extractor BaseSpace Data Ecosystem Browser Other Future Apps AB Sciex

3 SWATH Acquisition to MRM Validation SWATH to MRM Builder App in OneOmics Project Transition list to accelerate MRM assay dev Assembler Filter for differential proteins Extract key info from SWATH data *.qmethod for processing SWATH or MRM data Select differential proteins to verify (filter by fold change or list of accession #) Automatically extract Q1, Q3, RT, reproducibility and intensity information from SWATH results to accelerate MRM assay development Close the bridge between SWATH discovery / verification and MRM validation AB Sciex Biomarker Discovery Biomarker Verification Biomarker Validation

4 Getting Started! Sample project available to get started AB Sciex

5 Analysis in BaseSpace Launch application to get the input form As with every BaseSpace application, user can specify an analysis name and add a description AB Sciex

6 Input Information Select the Results *.fcresult file generated by the Assembler Source of protein fold change, fold change confidence and reproducibility (MLRweight) that will be used filtering and peptide/transition selection Select the ion library.txt file used by the Extractor app Source of Q1 and Q3 information and RT information Select the Variable Window Input File used for acquisition Source of m/z boundaries for each SWATH window. Required only if you wish to generate a MultiQuant Software *.qmethod file for SWATH Acquisition data processing AB Sciex

7 Protein Selection Build Assay for Specific Subset of Proteins Build MRM assay for just differentially expressed proteins or list of specific proteins Select a.txt file with one protein per row The.txt file must be in the same project as the Assembler app results If field is blank, the protein controls below are used to determine protein set AB Sciex

8 Protein Selection Build Assay for Differentially Expressed Proteins Min protein fold change Set >1.0 to require a minimum fold change at the protein level For example, a value of 2.0 would only include proteins with ratios greater than 2.0 or less than 0.5 Requires at least one group comparison ratio to be as extreme as the threshold Minimum confidence in protein fold change Set value between 0 and 1 to filter proteins for assay, typically 0.75 is used For more info on computing protein fold change confidence, AB Sciex

9 Settings for MRM Assay Min and Max peptides per protein Set range of peptides Min and Max transitions per peptide Set range of transitions / fragment ions Setting these values higher than desired in the final MRM assay will allow some degree of refinement to happen during Skyline optimization Fractional weight placed on intensity in ranking to select best analytes: Set this to 1.0 to rank entirely based on intensity, 0 to rank entirely by most likely ratio confidence (MLRweight), or anywhere in between AB Sciex

10 Output Options 1. Simple Q1, Q3, RT simple text file 2. Skyline text file structured for direct import into Skyline Software 3. MultiQuant smrm qmethod file structured for direct import into MultiQuant software 4. MultiQuant SWATH qmethod - file structured for direct import into MultiQuant software. It is recommended not quantify more than ~ 30 peptides using this workflow. Finally, select the project to save the exports to AB Sciex

11 Conclusions SWATH to MRM Builder application in BaseSpace bridges the gap between SWATH discovery/verification and MRM validation This app enables: Easy transition of protein expression results from SWATH acquisition studies into targeted MRM assays Building of MultiQuant Software quantitation methods for processing Allows for multiple protein filtering options AB Sciex

12 Acknowledgements Sean Seymour Seymour Data Science, LLC AB Sciex

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14 Trademarks/Licensing For Research Use Only. Not for use in diagnostic procedures. AB Sciex is doing business as SCIEX AB SCIEX. The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective owners. AB SCIEX is being used under license. All rights reserved. Information subject to change without notice AB Sciex RUO-MKT A