Multiple_protease_proteolysis figure

[martinmayta]

Added a possible figure for the proteolysis section. If it is acceptable I can start working on a legend.

[jessegmeyerlab]

sorry for the slow reply @martinmayta. At the bottom right of the figure it says 'more single protein identifications' - I think you mean more identifications based on single peptides? If yes, is there a citation that demonstrates this? It seems likely true but we should back up that claim if possible. Also do you have a citation you can add to the main text for the claim that multiple proteases help identify more protein termini?

[martinmayta]

sorry for the slow reply @martinmayta. At the bottom right of the figure it says 'more single protein identifications' - I think you mean more identifications based on single peptides? If yes, is there a citation that demonstrates this? It seems likely true but we should back up that claim if possible. Also do you have a citation you can add to the main text for the claim that multiple proteases help identify more protein termini?

What I mant is "more unique proteins will be identified" due to enhanced coverage by multi enzyme proteolysis and unique peptides generated (see Miller, R. M., Millikin, R. J., Hoffmann, C. V., Solntsev, S. K., Sheynkman, G. M., Shortreed, M. R., & Smith, L. M. (2019). Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data. Journal of proteome research, 18(9), 3429–3438. https://doi.org/10.1021/acs.jproteome.9b00330). But if it is confusing I could rephrase it. How would you write it to be unequivocal? The same will happen with the N.termini identification. This was showm for small proteins in the paper: Kaulich, P. T., Cassidy, L., Bartel, J., Schmitz, R. A., & Tholey, A. (2021). Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides. Journal of proteome research, 20(5), 2895–2903. https://doi.org/10.1021/acs.jproteome.1c00115. Please let me know what do you think about it. Otherwise we can go more conservative and just affirm it increases coverage which will lead to more unique proteins identified and less protein group ambiguity.

[martinmayta]

sorry for the slow reply @martinmayta. At the bottom right of the figure it says 'more single protein identifications' - I think you mean more identifications based on single peptides? If yes, is there a citation that demonstrates this? It seems likely true but we should back up that claim if possible. Also do you have a citation you can add to the main text for the claim that multiple proteases help identify more protein termini?

@jessegmeyerlab Here there are other studies addressing the increased identifications when multiple proteaes were used. These one in plants: Vincent, D., Ezernieks, V., Rochfort, S., & Spangenberg, G. (2019). A Multiple Protease Strategy to Optimise the Shotgun Proteomics of Mature Medicinal Cannabis Buds. International journal of molecular sciences, 20(22), 5630. https://doi.org/10.3390/ijms20225630

These two in mammalian cell lines: (HeLa) Guo, X., Trudgian, D. C., Lemoff, A., Yadavalli, S., & Mirzaei, H. (2014). Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Molecular & cellular proteomics : MCP, 13(6), 1573–1584. https://doi.org/10.1074/mcp.M113.035170 (Jurkat) Giansanti, P., Aye, T. T., van den Toorn, H., Peng, M., van Breukelen, B., & Heck, A. J. (2015). An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas. Cell reports, 11(11), 1834–1843. https://doi.org/10.1016/j.celrep.2015.05.029

[jessegmeyerlab]

@martinmayta thanks for the additional information!

Maybe we can change the text in the figure to simply "more proteins"?

Can you also please add a paragraph near the beginning of the section that adds the points and citations from your comments here, and refers to your figure?

Make sure you add additional changes to your branch in this pull request - you can easily access it by clicking on the " add more commits by pushing to the main branch..." (See screenshot).

[martinmayta]

@jessegmeyerlab do you mean put "more proteins" or "more proteins identified"?

[jessegmeyerlab]

Either works for me.

On Tue, Mar 8, 2022, 3:32 PM martinmayta @.***> wrote:

@jessegmeyerlab https://github.com/jessegmeyerlab do you mean put "more proteins" or "more proteins identified"?

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[jessegmeyerlab]

@martinmayta thanks for updating the figure - a couple more requests before we merge this to the main version:

1. since you added a figure v3 instead of replacing v2 can you please update the text to point at the v3 figure
2. Can you please add a paragraph to this section adding the citations and justification for termini and protein IDs that you have in these comments?

[martinmayta]

Oh, I am sorry. I am new to Github and still learning. How can I update the figure so no confusion is made? I am out of town and cannot add the paragraph now but as soon as I go back and get my computer I will finish the task. Martin

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From: jessegmeyerlab @.> Sent: Thursday, March 10, 2022 3:24:11 PM To: jessegmeyerlab/proteomics-tutorial @.> Cc: martinmayta @.>; Mention @.> Subject: Re: [jessegmeyerlab/proteomics-tutorial] Multiple_protease_proteolysis figure (PR #27)

@martinmaytahttps://github.com/martinmayta thanks for updating the figure - a couple more requests before we merge this to the main version:

1. since you added a figure v3 instead of replacing v2 can you please update the text to point at the v3 figure
2. Can you please add a paragraph to this section adding the citations and justification for termini and protein IDs that you have in these comments?

— Reply to this email directly, view it on GitHubhttps://github.com/jessegmeyerlab/proteomics-tutorial/pull/27#issuecomment-1064362348, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUKY366ZLOPZ5NEQZPISYILU7I44XANCNFSM5P3UZWWA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[jessegmeyerlab]

No rush.

It's okay that you have multiple versions of the figure on GitHub but in the text where you refer to the file name it should match the file you want displayed. This is at the end of the figure legend text. Does that make sense?

On Fri, Mar 11, 2022, 6:47 AM martinmayta @.***> wrote:

Oh, I am sorry. I am new to Github and still learning. How can I update the figure so no confusion is made? I am out of town and cannot add the paragraph now but as soon as I go back and get my computer I will finish the task. Martin

Obtener Outlook para Androidhttps://aka.ms/ghei36

---

From: jessegmeyerlab @.> Sent: Thursday, March 10, 2022 3:24:11 PM To: jessegmeyerlab/proteomics-tutorial @.> Cc: martinmayta @.>; Mention @.> Subject: Re: [jessegmeyerlab/proteomics-tutorial] Multiple_protease_proteolysis figure (PR #27)

@martinmaytahttps://github.com/martinmayta thanks for updating the figure - a couple more requests before we merge this to the main version:

1. since you added a figure v3 instead of replacing v2 can you please update the text to point at the v3 figure
2. Can you please add a paragraph to this section adding the citations and justification for termini and protein IDs that you have in these comments?

— Reply to this email directly, view it on GitHub< https://github.com/jessegmeyerlab/proteomics-tutorial/pull/27#issuecomment-1064362348>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AUKY366ZLOPZ5NEQZPISYILU7I44XANCNFSM5P3UZWWA

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[martinmayta]

Yes, it makes sense. I will change the code to refer to v3. Thank you for all your revisions which will greatly improve the quality of the figure and text. Martin

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From: jessegmeyerlab @.> Sent: Friday, March 11, 2022 10:20:52 AM To: jessegmeyerlab/proteomics-tutorial @.> Cc: martinmayta @.>; Mention @.> Subject: Re: [jessegmeyerlab/proteomics-tutorial] Multiple_protease_proteolysis figure (PR #27)

No rush.

It's okay that you have multiple versions of the figure on GitHub but in the text where you refer to the file name it should match the file you want displayed. This is at the end of the figure legend text. Does that make sense?

On Fri, Mar 11, 2022, 6:47 AM martinmayta @.***> wrote:

Oh, I am sorry. I am new to Github and still learning. How can I update the figure so no confusion is made? I am out of town and cannot add the paragraph now but as soon as I go back and get my computer I will finish the task. Martin

Obtener Outlook para Androidhttps://aka.ms/ghei36

---

From: jessegmeyerlab @.> Sent: Thursday, March 10, 2022 3:24:11 PM To: jessegmeyerlab/proteomics-tutorial @.> Cc: martinmayta @.>; Mention @.> Subject: Re: [jessegmeyerlab/proteomics-tutorial] Multiple_protease_proteolysis figure (PR #27)

@martinmaytahttps://github.com/martinmayta thanks for updating the figure - a couple more requests before we merge this to the main version:

1. since you added a figure v3 instead of replacing v2 can you please update the text to point at the v3 figure
2. Can you please add a paragraph to this section adding the citations and justification for termini and protein IDs that you have in these comments?

— Reply to this email directly, view it on GitHub< https://github.com/jessegmeyerlab/proteomics-tutorial/pull/27#issuecomment-1064362348>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AUKY366ZLOPZ5NEQZPISYILU7I44XANCNFSM5P3UZWWA

. Triage notifications on the go with GitHub Mobile for iOS< https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android< https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub . You are receiving this because you were mentioned.Message ID: @.***>

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