MSTemplate_Creator

MSTemplate_Creator is an excel template providing users with a friendly interface to create different metadata annotation templates from mass spectrometry analysis results, which are suited for subsequent automated data processing and statistical analysis. To ensure integrity of the metdata, MSTemplate_Creator allows to read in MRM data files exported from mass spectrometry software, and provides macros to valide the metadata.

Table of Content

• MSTemplate_Creator
• Table of Content
• Meta
• Overview
• Starting Up
• Using Transition_Annot Sheet
• Using ISTD_Annot Sheet
• Using Sample_Annot Sheet

Meta

• We welcome contributions from general questions to bug reports. Check out the contributions guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
• License: MIT
• Think MSTemplate_Creator is useful? Let others discover it, by telling them in person, via Twitter or a blog post. Do use the 🙌 Show and tell under the GitHub Discussions and give this repository a star as well.

• If you wish to acknowledge the use of this software in a journal paper, please include the version number. For reproducibility, it is advisable to use the software from the Releases section in GitHub rather than from the main branch.
• To date, the software is only able to take in the following files exported from the following software.
  • csv files from Agilent MassHunter Quantitative Analysis Software
• Refer to the NEWS.md file to see what is being worked on as well as update to changes between back to back versions.

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Overview

For an overview on how the tool works, take a look at the Summary and Familiarisation file in the documentation page.

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Starting Up

Go to the Releases section in GitHub.

Download the zip folder. Unzip the folder, double click on the excel macro file MSTemplate_Creator.xlsm to start.

Upon opening you may encounter this security warning. Click on Enable Content so that the macro in the file will be activated.

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Using Transition_Annot Sheet

Load transition names from Agilent MRM data in csv file with Load Transition_Name from Raw Data

Load transition names from tabular data in csv file with Load Transition_Name from Table Data

Check the internal standards with Validate ISTD.

Once validated, transfer the internal standards to sheet ISTD_Annot with Load ISTD to ISTD_Table

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Using ISTD_Annot Sheet

Key in the concentration of the internal standard and convert to nM or other units to verify. Unit values under the column Custom_Unit can be used later to obtain the sample unit of concentration.

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Using Sample_Annot Sheet

Load sample names from Agilent MRM data in csv file with Load Sample Annotation from Raw Data.

Use Autofill ‘Sample’ in Sample_Type to fill empty cells under the Sample_Type column with “SPL”

It is possible to merge Agilent MRM data with a sample annotation file in csv.

Load sample names from tabular data in csv file with Load Sample Annotation from Table Data. Use Autofill ‘Sample’ in Sample_Type to fill empty cells under the Sample_Type column with “SPL”

Next, fill in the Sample_Amount, Sample_Amount_Unit and the ISTD_Mixture_Volume_[uL] columns. If a particular Sample_Type has consistent inputs, the Autofill by Sample_Type button helps to fill in these consistent values quickly.

To obtain the analyte’s concentration unit measured in each sample, go the Sample_Annot sheet and fill in the Sample_Amount_Unit for each sample. Next, on the ISTD_Annot sheet, select the concentration unit of the internal standard to use under the Custom_Unit column. Return to the Sample_Annot sheet and use Autofill Concentration_Unit to fill in the Concentration_Unit column.

Transfer Sample with QC sample type of “RQC” to Dilution_Annot sheet with Load RQC Samples to Dilution_Table

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