Input data and parameters

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Automatically identify and extract peak retention times
Molecule: Standard Retention times: to
Molecule: Retention times: to

Processed peak areas

Instructions for using this page:

1. Make sure you have the MSDChemStation report file from the Agilent GC-MS control system, and an associated Excel spreadsheet defining metadata for the samples.

2. If you already know what specific retention times define the peaks of interest, uncheck the box labeled "Automatically identify and extract peak retention times" and enter the upper and lower bounds for each peak to be extracted, along with the molecule names.

3. Once you have entered retention times - or if you want the program to identify peaks for you - drag in the GC-MS report file.

4. You should also upload the Excel spreadsheet using the same form (this can be done at any time).

5. If the report is processed successfully, the section below will be populated with summary information and a table allowing you to edit the processed report. Please pay special attention to any sample or peak marked by a red triangle - these indicate that additional peaks were found in the given range.

6. If you want to normalize peak areas using the standard in each sample, click the button "Calculate relative peak areas". You may reset the table to the original extracted values at any time by clicking "Reset table".

7. Once both the report and the Excel key are loaded, click "Finalize and continue" to merge the processed peak areas and metadata. The server will then generate an Excel spreadsheet that will be downloaded to your computer.