PepSee 2.8 Beginners Guide

March 2018

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Toolbar Segment headers

Column headers

Actions& Identi- fication

Data (Assay, Properties, Batch…)

Sequences

Freely sizable segment areas

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start a new, empty project

load existing project (pepsee, csv, xls)

import data (FASTA, PLN, txt), filter duplicates

save project to disk

create Excel report

create charts

To begin we will load some example data from an xls. (Sample data available at https://www.biosolveit.de/PepSee/download/pepsee_sample.xlsx)

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PepSee will add the sequences automatically to the sequence tab and assay data to the data tab. If the data is hard to read for you Please adjust the font size with the slider in the lower right corner.

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To design a new sequence click on the “lego” brick. This will append a new row to your table. Simply start adding a new sequence by typing the one-letter code into the sequence table. Use the Shift-key to enter dextrorotatory amino acids. It will be useful to add an identifier to the new sequence in the left section and of course assay data, if available, by double-clicking to the field.

Start typing here Name here

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Advanced peptide design:

To insert special amino acids: hit the „X“-key and select from the dropdown

To create cyclizations and bridges: select the start- and end-points, then right click on the selected sequence part. Possible cyclisations are: Disulfide: C – C; X - X Thioether: [C,M] - [S, T, Y, D, E]; X - X Cycle: n-term - c-term; [D, E] – K; n-term - [D,E]; K - c-term; X – X; n-term – X; or X - c-term

Hint: Selecting parts of any peptide sequence in PepSee and using Ctrl-C and Ctrl-V enables you to copy and paste sequences

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When you are ready designing your protein click on the lego brick at the left side and toggle the editable state. The green highlighting of the row will disappear then. By clicking on the lego brick in this column you can make the respective “old” sequence editable as well.

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To perform a multi-sequence alignment click on the alignment button in the segment header. If you want to align all sequences to one reference, mark your reference in the first column.

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The reference column is highlighted in orange. You can change the coloring of the sequences with the buttons on the top right.

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Standard amino acid coloring: no reference selection needed • Yellow = hydrophobic • Green = polar • Blue = basic • Red = acidic

Reference coloring: Dark blue = exact match to reference Light blue = match in same amino acid group Grey = no match to reference

Correlation coloring: Select a reference row Select Assay column and thresholds using

dialog via dropdown Only building blocks where a change was

introduced are colored with regard to changed Assay values in green-to-red gradient

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Show / Hide /Add columns: • Right-click the Segment-Header

Filter column values: • Right-click the Column-Header

Pattern highlighting: • Select by using Drop-Down Menu • Enable by clicking “Pattern”-Button

Sort by column: • Left-click on the Column-Header

Basic functionalities are:

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By right-clicking on a sequence position you can filter as well for special amino acids or groups of amino acids at this position. All filters will appear at the top. You can either delete them (with the X) or deactivate them with the slider to keep them for later.

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Add or edit annotations by clicking the „Pen“ icon in the Annotations column and write to the post-it. Rows containing annotations get a little „pen“ attached.

Select Favorites by marking them with a „Star“. You can filter by these columns, as well.

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Reporting - Charts Access interactive Charts by using the toolbar

Scatterplot Radarplot

Select numeric value Axis by clicking on them

Plot allows selecting Favorites by clicking on data points

Select numeric value Axis by selecting them on the side bar

Displayed areas are based on selected favorites

Hovering over data points and areas shows the identifier and underlying values

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Reporting – Export to Excel

Generate comprehensive Reports using the toolbar

Exports current project „view“ as is to xlsx

Export contains multiple sheets with the various sections and all data, as well peptide sequence images for publications.