Data insertion

Dialog window

Use the dialog window to paste data manually. Amino acids in the sequence string have to be in the form of single letter codes. It makes no difference if the string is expressed in lowercase letters or in capital letters. Spaces and hard returns at line endings (Enter key) are allowed. A warning is displayed when the pasted sequence contains unacceptable symbols.

Import from a file

To import data from a file, the respective source may be selected on one's computer using the input form. After choosing the file, an automatic control will be launched to check out the possibility of import. When the file has been read and approved, a text will be displayed as follows: "file name of the file ready to load". Clicking "load from file" button will execute the import. The supported input formats are TXT and FASTA.

Sequence-deduced protein properties and Transcription of DNA sequences

A continuously updated information calculated from the pasted sequence string is displayed next to the dialog window (on the right). There are monoisotopic and average molecular mass, chain length, index of hydropathy, NPS (content of non-polar residues) and isoelectric point shown.

To rewrite the DNA sequence click the "Rewrite DNA seq."

Statistics

Button "Compute Statistics" show informations about sequence.

Options

Ionization

You may select the appropriate ionization mode; the respective calculation will consider adding or subtraction of proton mass (1.0073 Da).

Cysteine modification

This selection counts with a fixed carboxymethylation (Cys_CM) or carbamidomethylation (Cys_CAM) of all cysteines in the input sequence. Cys_CM represents an increase in the monoisotopic and average masses of 57.02 Da and 57.05 Da, respectively, per each cysteine. Cys_CAM represents an increase in the monoisotopic and average masses of 58.01 and 58.04, respectively, per each cysteine.

Methionine oxidation

This selection counts with a variable oxidation of methionine and computes all possible variants. Each oxidized methionine represents an increase in the monoisotopic and average masses of 15.9949 Da and 15.9994 Da, respectively.

Missed cleavage

This option simulates possible missed cleavages. All combinations will be displayed in the output list.

Cutting rules

Cut by enzyme

This option means to apply predefined cutting rules. The corresponding group of rules is defined directly by the selection of a proteolytic enzyme (or a specific reagent like CNBr or formic acid). Other defined rules are then blocked.

Cut by user-defined rules

The user can use the configurator to set his/her own cutting rules or to write the rules directly into the command line.

The user can remove own cutting rules or to add another.

Setting-up filters

If necessary, it is possible to select filters for arranging the output list. Clicking the button "Click to Show/Hide filters" will display the setup menu. Repeated clicking hides the menu. The selected filter setting remains active even after the hiding.

For each filter, one may select a condition for the criteria and value. The values are taken from a closed interval i.e. including the value. All conditions have to be met to allow viewing the filtered segment.

Execution of cutting and filtration of results

Program execution (performing the requested cut and filtration of results) will be launched by clicking the button "compute cut". Form wil be reseted by clicking the button "reset form".

Results

Listing of results

Each row shows one of possible cleavage peptides. The first column shows the peptide position in the input sequence. In the case of multiple occurrence, all possibilities are listed. Clicking the link "another cut" will place the peptide sequence into a new dialog window to perform further cutting.

Sorting of results

The default setting displays the results by peptide position in the input sequence. In case of request for another kind of sorting, the user may select one of the available sorting buttons. First click means ranking the results in ascending order, one more clicking provides descending order.

Printing out the results

Prior printing out the results, the user may hide the dialog window by clicking the button "Hide input form". It is activated back by clicking the button "Show input form".