Feedbacks on the cluster summary page

[ruiwanguk]

@jadianes I cannot state enough that how nice it is to see the new shiny cluster summary page, really nice work there.

Below are some comments, these are only some ideas:

• May be make the "Primary peptide" as a separate section as the Summary section, and also add a section for modifications on the right hand side.
• In the summary section, merge Precursor m/z with Precursor charge.
• In the summary section, may be we can add tooltips to explain what each set of numbers mean
• In the summary section, the bullet chart for max ratio looks a bit strange, may be it is just me
• In the summary section, may be we can change “Max Ratio” to “Peptide Ratio"
• In the original projects section, the page number are shown as strange characters
• In the original projects section, I feel that it is probably better we lay out the content horizontally, but this is just my preference.
• In the original projects section, the title of the project can be truncated
• In the original projects sections, I would probably show the title and the description together
• Remove “distribution” from “Species Distribution”, “Modification Distribution”, “Precursor M/Z distribution”, and “Spectrum similarity distribution"
• In modification distribution section, “NaN” is current displayed in the popup tooltip.
• Move Unique peptides section above cluster quality related distributions (Rui will provide updated mockups)
• Change the breadcrumb to “PRIDE > PRIDE Cluster > Cluster Details"
• It would be nice to change how we page the unique peptides

[ruiwanguk]

[jgriss]

@jadianes This is great work! We're 90% there!

Comments:

• Add possibility to download consensus spectrum as MGF
• Some peptides contain "[Mod name] at position" (see screenshot)
  
• There is a rendering issue of the project summaries (Firefox 36.0.1 on Ubuntu)
  
• I agree with all of Rui's points
• I'd put the precursor m/z and charge after the primary peptide sequence (ABCDE @120m/z, 1+)
• is it possible to add the number of projects to the "Unique peptides" table?
• sort unique peptides according to number of psms in descending order (most common peptide should be on top)
• highlight most common peptide in unique peptide table
• visualization of "max ratio" is confusing to me
• limit digits of max ratio tooltip (or number of rendered as text)
• I do not understand the "M / N" numbers in "Summary", I guess "M" represents the number for the most common peptide and "N" the total number for the cluster?
  • if this is the case, this does not make sense for modifications
• highlight modified residues in peptide sequence (unique peptides table and heading), a tooltip displaying the modification on the modified AA would be ideal (method used in original web interface)
• buttons changing the number of unique peptides being displayed are confusing to me if there are <10 peptides displayed

[jadianes]

@ruiwanguk @jgriss thanks a lot for the detailed feedback! I'll start working on this today!

[jadianes]

@ruiwanguk I've just committed a version with the layout you suggested in your mockup

[ruiwanguk]

@jadianes thanks a lot, we will deploy a new version of the webapp

[jadianes]

@ruiwanguk @noedelta it might be a good idea if we review the current deployment and make a new list of feedback ordered by priority. Also it would be nice if we define a threshold in that list for those things that are indispensable for the first release milestone.

And it would be great if somebody else helps with this. Exactly the same applies to the search results page :).

[jadianes]

@ruiwanguk what goes into the first modifications section? Are we keeping the second modification section (the distribution one)? Are we keeping the same title in both of them?

[jgriss]

@jadianes @ruiwanguk @noedelta Hi! I agree with Jose. I think we need to review everything and have to define the "must haves".
About the new layout:

• I'd not separate the sequence of the primary peptide and the modifications into two sections. Again, highlighting the mods in the sequence seems the most natural form of presentation to me (this is the way it's done in most tools / search engines). Our users will be most familiar with this view (in my opinion).
• Again, I'd add precursor and charge information to the peptide sequence

[jadianes]

@jgriss could you give me some link or screenshot so I have a reference of how a sequence with highlighted mods looks like? I have the feeling that this would be a good improvement on the UI since it will save some space and communicate that more information in a more accurate way.

[jgriss]

@jadianes This is the way it is represented in the original version:

Alternatively (or even nicer) one could show the modification's name instead of only the mass delta in the popup
Terminal modifications are displayed within the brackets before or after the sequence (as in this example)