Library Generators

Build your calibration workflow in sequence

This page is used for Step 1 and Step 2 of the GC-AutoFit calibration pipeline. Choose the output you need, then upload a single ZIP containing the required spectra and CSV templates in .CDF or .mzXML format.

Step 1

Retention Index (RIs) Library Generation

Alk-std.mzML + mass_spec_ris.csv template with expected RTs

Output:mass_spec_ris.csv with filled reference RIs

Step 2

Calibration Equation Library Generation

Alk-std.mzML + mass_spec_ris.csv + Cal1.mzML-Cal9.mzML + theoretical_calibration_concentrations.csv

Output:calibration_equations.csv

Step 3

Quantify Unknown Samples of Interest

Alk-std.mzML + mass_spec_ris.csv + calibration_equations.csv + Samples

Output:Final concentrations per sample per analyte

Handled on the Quantify Samples page

Choose the generator submodule for your library

Step 1

Generate filled mass_spec_ris.csv - RI Library Generation

Use this when you have alkane standards and a mass_spec_ris.csv template with expected RTs.Retention Indices are generally more transferable across different GC methods than calibration equations, so this is a good first step to take even if you ultimately want calibration equations.

Alkane Standards + Expected RTsmass_spec_ris.csv with filled RIs

Step 2

Generate calibration_equations.csv - Calibration Equations Library

Use this when you already have a filled mass_spec_ris.csv from Step 1 and want to generate calibration equations. At least 6 calibration samples are required. Currently, we only support automatic fitting of linear equations only. Non-linear options coming soon!

Alkane Standards + RI Library + Calibration Samplescalibration_equations.csv with fitted equations

Upload Package

Upload one ZIP file containing the required spectra and CSV files for the step you selected. All files must be at the top level of the ZIP and follow the naming conventions described in the instructions. Up to 9 calibration spectra are recommended per metabolite for Step 2.

ZIP contents required for both steps

Include an alkane standards spectrum named alkstd.CDF or alkstd.mzXML. You may also include an optional blank spectrum such as Blank.mzXML or Blk.mzXML.

For Step 1

Include your completed mass_spec_ris.csv template with expected retention times so the pipeline can calculate reference RIs.

mass_spec_ris.csv template only
Example ZIP for Step 1 (alkstd.mzXML + mass_spec_ris.csv)

For Step 2

Include mass_spec_ris.csv from Step 1, theoretical_calibration_concentrations.csv, and calibration spectra named cal1-cal9 with either .CDF or .mzXML extensions.

theoretical_calibration_concentrations.csv template only
Example ZIP for Step 2 (mass_spec_ris.csv + theoretical_calibration_concentrations.csv + cal1.mzXML-cal9.mzXML)

Zip file

Drag and drop your ZIP package here

or click to browse for the upload file

No file selected

File formats required in the zipped file:

Template files:

must be named mass_spec_ris and/or theoretical_calibration_concentrations
.csv

Sample files:

must be named alk-std or alkstd for the alkane standards spectrum, and cal1 through cal9 for the calibration spectra
.CDF, .mzML, .mzXML

Package all files into a single .zip with the files stored at the first level.

Internal Standard

Biofluid

MF (Match Factor) Score Cutoff

An integer between 0 and 999. A range between 400 and 600 is usually appropriate.