Figure discussion

[jessegmeyerlab]

Use this thread to discuss potential figures. I think we need about one figure per section depicting the key concept from that section.

@Arokiarex is drafting a figure for the quantitative strategies or metabolic labeling section.

Here are thoughts for the other sections:

1. Introduction - graphical giving details of the general steps that might be performed in bottom up proteomics
2. Types of experiments - ?
3. Protein extraction - ?
4. Proteolysis - figure depicting how primary sequence of a protein will be cleaved by various proteases, and how some of the proteases would give additional coverage
5. protein/peptide labeling - figure in progress by Rex @arokiarex showing general quantitative strategies
6. enrichment - cartoon showing various strategies for enrichment
7. peptide purification - cartoon showing concept of removing contaminants with various methods
8. mass spectrometers - show different geometries
9. peptide ionization - show cartoons of ESI and MALDI ionization
10. data acquisition - show scan types as cartoon
11. raw data analysis - show concepts of how peptides are identified and quantified
12. biological interpretation - show example of biological analysis: volcano plots, network analysis, GO term enrichment
13. experiment design -?

[ArokiaRex]

Hi All,

I have a small suggestion. First, let's segregate our work on figures so there won't be any repetition on the same sections.

I (Rex) will be working on Section 12. Biological interpretation figure. I will complete it on or before 23rd January 2022.

Thanks Rex

[dschust-r]

Hi everyone,

I just added some figures for Section 9. Peptide Ionization.

[martinmayta]

Ok. Which other figures are currently being made? So as not to superimpose with anybody.

[jessegmeyerlab]

Ok. Which other figures are currently being made? So as not to superimpose with anybody.

@ArokiaRex is drafting a figure for the protein/peptide enrichment section, that is the only figure I am aware of in progress

[martinmayta]

Ok, I have done a possible Figure 4. Let me know what do you think and if I could upload it to the manuscript t

[martinmayta]

How can I become a contributor to the proteomics tutorial repository to upload material @jessegmeyerlab ?

[jessegmeyerlab]

How can I become a contributor to the proteomics tutorial repository to upload material @jessegmeyerlab ?

I love this figure, thanks!

Please check out the information here about how to contribute, and let me know if you have any questions: https://github.com/jessegmeyerlab/proteomics-tutorial#how-to-contribute

[dschust-r]

Hi @martinmayta,

Maybe check the peptides in the upper part of the figure again. I think you mixed up the cleavage sites (e.g. trypsin cleaves C-terminally of Arg/Lys and would result in a peptide like this: -------K).

[martinmayta]

Hi @dschust-r thanks for noting that. Indeed they were all shifted left to right and viceversa. I corrected that.

[martinmayta]

[martinmayta]

How can I become a contributor to the proteomics tutorial repository to upload material @jessegmeyerlab ?

I love this figure, thanks!

Please check out the information here about how to contribute, and let me know if you have any questions: https://github.com/jessegmeyerlab/proteomics-tutorial#how-to-contribute

Thanks @jessegmeyerlab I did a pull request but I get this message: "1 workflow awaiting approval First-time contributors need a maintainer to approve running workflows" What can I do?

[martinmayta]

Hi everyone,

I just added some figures for Section 9. Peptide Ionization.

@dschust-r How did you linked the text for the figure to the figure itself in the repository?

[dschust-r]

@martinmayta I added the figure to the images folder and linked it in the code with:

![**Figure title**
Figure description.](images/yourfigure){#fig:figure-description tag="1" width="100%"}

For one of my figures this looked like this:

![**MALDI**
The analyte-matrix mixture is irradiated by a laser source, leading to ablation. 
Desorption and proton transfer ionize the analyte molecules that can then be accelerated into a mass spectrometer.](images/MALDI.png){#fig:MALDI-mechanism tag="1" width="100%"}

[jessegmeyerlab]

Sorry for the slow reply!

Thanks @dschust-r for your help teaching how this works, and thanks @martinmayta for updating the figure. Looking at the PR now

[martinmayta]

Is anyone working on the DIA/DDA figure?

[jessegmeyerlab]

Not that I know of. It's all yours!

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Is anyone working on the DIA/DDA figure?

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[ger225]

Hi, I just made a pull request on network analysis. I am working on a figure that I´ll upload here for now. I still need to link to it in the manuscript.