What can produce "Cannot recalibrate" error in Label-Free Quantification for Proteome Discoverer 3.0?

13 April 2023 1 577 Report

I am trying to perform Label-Free Quantification in Proteome Discoverer 3.0.

I am comparing sample files, I set the provided Processing and Consensus Workflows .

For Grouping & Quantification I generated simply the ratios of F4-6 and F3. Running the job results in Execution Failed state, with warning "Cannot recalibrate file F3, because there are no spectra!". (See files attached)

At this point I am stuck. Maybe it is just a trivial thing that I am missing.

Thank you for your suggestions.

In my sample files the meta information, number of MS2 scans is 0, could it mean that the second acquisitioin method is missing?

Kenneth Kipsang

The "Cannot recalibrate" error in Label-Free Quantification for Proteome Discoverer 3.0 can be caused by several factors, including:

Incorrect or missing calibration data: Label-Free Quantification relies on accurate mass measurements to quantify proteins. If the calibration data is incorrect or missing, the software may not be able to accurately calculate protein concentrations.

Poor quality data: Poor quality data can lead to inaccurate mass measurements, which can in turn lead to errors in Label-Free Quantification.

Software issues: The error message could also be due to issues with the Proteome Discoverer 3.0 software itself. This could be due to a bug or a compatibility issue with the user's system.

Sample preparation issues: Issues with sample preparation, such as incomplete digestion of proteins or contamination, can also lead to inaccurate mass measurements and errors in Label-Free Quantification.

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