The TCellXTalk database can be queried for either proteins or peptide sequences of interest using the Search section.
Proteins can be searched using a text field that enables searches by
the UniProt ACcession Number (e.g., "P16402"), the UniProt ID (e.g., "CYC_HUMAN")
or words included in the UniProtKB protein description (e.g., "kinase").
The wildcards "*" for "one or more" unknown letters (e.g., "P16*"), and "?" for "only one" unknown letter (e.g., "P164?5") can also be used.
Multiple proteins can be searched in batch entering, in the text-area field, their UniProt ACcession Numbers separated by spaces, commas or semi-colons.
In this case, wilcards cannot be used.
All proteins in the database can be browsed pressing the | Browse All Proteins | button.
Alternatively, the database can be queried for peptides containing a
certain sequence of interest. Peptide sequences must be entered using the amino
acid 1-letter code.
The wildcards "*" and "?" can be used for "one or more" or "only one" unknown amino acids, respectively.
Options for inference of peptides
In the protein detail view, TCellXTalk allows the generation of potential
co-modified peptides by in silico protein digestion and subsequent filtering
of peptides with PTM combinations based on user-specified digestion enzyme,
peptide length, number of PTMs and required PTM type(s).
The resulting list of co-modified peptides can be readily accessed or downloaded as a tab-separated values (TSV) file which can be imported in any spreadsheet program.
Three different proteases can be used for protein digestion: (i) “GluC”, (ii) “Trypsin” (with canonical trypsin specificity) or (iii) “Trypsin with exceptions”, which allows a missed cleavage when the sequence contains two consecutive lysine and/or arginine residues.