First things first here is a link the tool itself: mzCutCut
The tool allows you to quickly predict the peptides that would be produced by digesting an amino acid sequence with trypsin (and in the future other proteolytic enzymes).
When you first open the page you'll see the primary search bar at the top along with 2 buttons "search" and "upload".
If you want to search for a protein sequence from uniprot, you can enter in any terms into the search bar and either press the enter key or the search button to reveal a list of options suggested by UNIPROT.
Once you click one of the presented options, the sequence will appear in the main edit window and the program will automatically calculate peptides along with their masses which will appear in the bottom table.
If you perform multiple UNIPROT searches, the sequences you select will be placed into multiple editing windows that you can access by scrolling. All actively present sequences will be used for digestion and the predicted peptides will be aggregated in the table at the bottom of the page.
The main edit window allows you to paste in any amino acid sequence and edit it. Any edits you make to the sequence will immediately trigger an update to the peptide calculations that are shown below. Below the main edit window are a number of parameters you can adjust with regards to the digestion and the filtering of the resulting peptides.
The enyme option allows you to slect the enzyme used for digestion. Only trypsin is available at the moment, but this might change in the future. The max missed cleaveges specifies the maximum number of missed cleavages that will be considered when constructing the list of possible peptides from the digestion. Below are the filtering options. You can filter by the number of amino acids (length) of the peptides, by their mass over charge ratio (m/z) where z = 1 and by a pattern of amino acids. As an example entering a pattern of "CY" will leave only peptides that contain a cysteine followed by a tyrosine. Any changes made to the filtering criteria will immediatley be reflected in the peptide table below.
You can sort the table by a particular column by clicking the corresponding column header. Multiple clicks will change the direction of sorting. Multiple column sorting is also supported and can be done by holding shift down when clicking subsequent column headers. You can search the table for specific peptides by using the search field. You can search for a particular sequence, location, m/z, etc.
You can download the peptides produced by the digestion by clicking one of the two download options. As the names imply, clicking "download filtered peptides" will produce and download a CSV document that contains only the peptides that passed the filtering criteria you used above. Similarly, clicking "download all peptides" will produce and download a CSV document that contains all peptides from all sequences.
The tool also allows for bulk digestions via the upload button to the right of the search bar at the top of the page. One option is to upload a CSV file containg a single column of UNIPROT identifiers which will trigger the systematic download of all corresponding canonical sequences associated with those IDs from uniprot. The second option is to upload a FASTA file containg multiple protein sequences. If the number of sequences is below 1000, these sequences will be processed and show up as a list of editable sequences in the area below. You can then use the tool as described above. If the amount of sequences uploaded exceeds 1000, the editing window will automatically disappear along with the peptide table. You can still change filter paramters but these changes will only be reflected in the downloaded files.