Thanks Kelstrup for your very careful reading.
Answer to 1st question: For LTQFT, we have recorded the full MS scan in centroid mode to save disk space since 2006 when the disk was still expensive. I understand your concerns about the effect of data recording mode. Actually, we also applied the same strategy to high-resolution proteomics and phosphoproteomics data recorded in profile mode (both MS1 and MS2) from latest Q Exactive, the conclusion remains the same, i.e. correction of spectrum extraction errors results in a siginifcant increase of peptide identification. We did not include it in this paper since it did not affect the conclusion, but definitely increase the length of the paper.
Answer to your 2nd question: It is true that MaxQuant and Raw2MSM are designed specially for high-resolution data recorded in profile mode. However, according to our test, they performs equally well on data recorded in centroid mode. For example, the accuracy of the monoisotopic peak selection is over 90%, better than other tested software. As you know, only a few parameters can be modified in these two software. We evaluated it and selected the best if it is not the default.
I am a bit surprised that fulll MS scans were acquired in centroid mode when Thermo's centroiding software is somewhat lacking? Anyone know why one would do that, especially for a purpose such as this? Disc space is cheap nowadays compared to an instrument I think?
Second question: These tools may have settings for recognizing peak shapes (I know MaxQuant and Raw2MSM do) - could this somehow be optimized for the given setting? Sometimes space-charging or other non-linear effects make the default settings less optimal.
Otherwise, I liked the study goal. Not enough people are looking at the data any more