The Proteoform Finder workflow

The Proteoform Finder workflow is designed to perform targeted quantitation of proteoforms from intact SIM and MRM experiments.

The Proteoform Finder workflow is partitioned into Selected Ion Chromatograms, Intact Isotope Fitting, and Top-Down workflows.

Create the Selected Ion Chromatograms workflow

The Selected Ion Chromatograms workflow only contains the Proteoform Finder tab.

From the Home screen, select the Proteoform Finder > Selected Ion Chromatograms workflow.
In the Experimental Design tab, select Add Files, select Individual Data Files, navigate to the folder containing the desired files, select them, then select Open.
In the Settings tab, adjust the settings if needed.
Select the Targets > Masses tab, then select Import Targets, navigate to the folder containing the desired spreadsheet folder, and select Open.
Select the Targets > Proteoforms tab, then select Import Targets, navigate to the folder containing the desired spreadsheet folder, and select Open.

Note: Alternatively, select Add Target, name and fill in the sequence, then select OK to add a custom proteoform.
In the Data Processing tab, select Process Files.
Review the results in the Charts, Spectra, Fragments, and Charge States tabs.
Select Export to export the results as a spreadsheet.

The Intact Isotope Fitting workflow only contains the Proteoform Finder tab.

From the Home screen, select the Proteoform Finder > Intact Isotope Fitting workflow.
In the Experimental Design tab, select Add Files, select Individual Data Files, navigate to the folder containing the desired files, select them, then select Open.
In the Settings tab, adjust the settings if needed.
Select the Targets > Masses tab, then select Import Targets, navigate to the folder containing the desired spreadsheet folder, and select Open.
Select the Targets > Proteoforms tab, then select Import Targets, navigate to the folder containing the desired spreadsheet folder, and select Open.

Note: Alternatively, select Add Target, name and fill in the sequence, and select OK to add a custom proteoform.
In the Data Processing tab, select Process Files.
Review the results in the Charts, Spectra, Fragments, and Charge States tabs.
Select Export to export the results as a spreadsheet.

The Top-Down workflow only contains the Proteoform Finder tab.

From the Home screen, select the Proteoform Finder > Top-Down workflow.
In the Experimental Design tab, select Add Files, select Individual Data Files, navigate to the folder containing the desired file, select it, and select Open.
In the Settings tab, adjust the settings if needed.
Select the Targets > Masses tab, then select Import Targets, navigate to the folder containing the desired spreadsheet folder, and select Open.
Select the Targets > Proteoforms tab, then select Import Targets, navigate to the folder containing the desired spreadsheet folder, and select Open.

Note: Alternatively, select Add Target, name and fill in the sequence, and select OK to add a custom proteoform.
In the Data Processing tab, select Process Files.
Review the results in the Charts, Spectra, Fragments, and Charge States tabs.
Select Export to export the results as a spreadsheet.