The UNIFI Intact Protein workflow and the INTACT Mass application processing results are different - WKB271690

SYMPTOMS

• When analyzing the same data with the same integration parameters in the Intact Protein workflow in the UNIFI app and the INTACT Mass app, the two sometimes give different integration results

ENVIRONMENT

• waters_connect
• INTACT Mass, protein analysis
• UNIFI, intact protein workflow

CAUSE

Background subtract is not enabled in the UNIFI processing method.

Background subtraction is enabled by default in the INTACT Mass app, so to truly compare like with like when analyzing the same data in INTACT Mass and the UNIFI intact protein workflow, you must enable background subtraction in the UNIFI analysis method.

The majority of the difference between the INTACT Mass peak height and peak area results and the equivalent result in UNIFI Intact Protein may be due to whether or not they have background subtract enabled in the UNIFI Intact Protein method. Without background subtract enabled, we get very different results processing the same data with the same parameters in INTACT Mass and in UNIFI. However, when we enable background subtract with automatic parameters, that gave almost identical results to those seen with INTACT Mass.

FIX or WORKAROUND

1. Enable background subtract in the UNIFI analysis method and select the 'Automatic' button in the background subtract options.

Results with background subtract enabled. 

ADDITIONAL INFORMATION

INTACT Mass and UNIFI use the same peak detection algorithms. However, the source code for the algorithms in UNIFI and the waters_connect applications is different and are likely to have diverged, which might affect the results. So even after enabling background subtract in the UNIFI processing method there may still be small differences in the results.