rev 1 - more motivation?

[rmflight]

In Results section 2.1. the authors are trying to demonstrate that the Xcalibur calculated intensities and theoretical peak intensities differ with the help of Figure 1. The observed and theoretical intensities often differ and it is well-known fact. What new things that authors are trying to show are hard to find. Figure 1 is hard to understand and there is not enough description of that.

I think the issue here is we don't redo Figure 1 with the intensities from SCPC put back as a comparison to what XCalibur produced. We talk about it in the abstract, and Figure 12 actually shows it, but not in the way that makes the case to the reviewer.

Should we have a Figure 12D that is Figure 1 and add in the SCPC peaks to show the improvement in fit to theoretical?

[hunter-moseley]

Robert,

We could add a Figure 12D, but that will not directly address the comment.

We need to add description of the importance that the deviations increase as the peak intensity gets lower.

Warm regards, Hunter

On Wed, May 11, 2022 at 2:49 PM Robert M Flight @.***> wrote:

In Results section 2.1. the authors are trying to demonstrate that the Xcalibur calculated intensities and theoretical peak intensities differ with the help of Figure 1. The observed and theoretical intensities often differ and it is well-known fact. What new things that authors are trying to show are hard to find. Figure 1 is hard to understand and there is not enough description of that.

I think the issue here is we don't redo Figure 1 with the intensities from SCPC put back as a comparison to what XCalibur produced. We talk about it in the abstract, and Figure 12 actually shows it, but not in the way that makes the case to the reviewer.

Should we have a Figure 12D that is Figure 1 and add in the SCPC peaks to show the improvement in fit to theoretical?

— Reply to this email directly, view it on GitHub https://github.com/MoseleyBioinformaticsLab/manuscript.peakCharacterization/issues/32, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEP7BZ7TFX2YNF6QHVIDMLVJP6MBANCNFSM5VV3TL6A . You are receiving this because you are subscribed to this thread.Message ID: <MoseleyBioinformaticsLab/manuscript.peakCharacterization/issues/32@ github.com>

-- Hunter Moseley, Ph.D. -- Univ. of Kentucky Associate Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Institute for Biomedical Informatics / UK Superfund Research Center Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still.

Email: @. (work) @. (personal) Phone: 859-218-2964 (office) 859-218-2965 (lab) 859-257-7715 (fax) Web: http://bioinformatics.cesb.uky.edu/ Address: CC434 Roach Building, 800 Rose Street, Lexington, KY 40536-0093

[rmflight]

On further thought, I think what may work better is showing the log(NAP_P1) - log(NAP_P2) ~ log(INT_P1) - log(INT_P2) and that it gets worse as one of the peaks is lower intensity / abundance.

So we would have (A) being the current plot, and (B) being the ratio plot?

[rmflight]

Or even have (B) be the plot of each peak, actual intensity vs theoretical intensity, or the ratio of theoretical to real plotted against the real intensity to show how the ratio changes as the intensity decreases.

[rmflight]

closed by 931554c0d0ae043113252f74373bf7eee473c8e1