Dear Xiaojing,

As you may know, most proteins are synthesized as “precursors” and undergo posttranslational processing (“maturation”) that may occur while translation is still continuing or after it is over. There are dozens of posttranslational modifications (e.g. phosphorylation, glycosylation, alkylation, etc.). For example, in eukaryotes, all protein synthesis starts with methionine, which is in many cases removed upon processing. Many precursors contain so called “signal” sequences that are also removed upon maturation. Protein databases (including NCBI) usually show sequences for unprocessed proteins (i.e.”precursors”) , many of which just don’t exist in “real life”. In order to find some information about posttranslational modifications for each individual protein, you may turn to UniProtKB database (Swiss Institute of Biotechnology; http://www.uniprot.org) which is one of the most comprehensive and manually annotated protein databases. You need to keep in mind, however, that beside well established modifications, they often mention some predicted ones (for example, modifications “by similarity”), and these latter not necessarily occur at all. In your particular case, kininogen-1 (what is the species? Let’s say, mouse protein): the precursor (661 residues) contains a signal 1-20, which is removed, then the rest (21-661) is cleaved into 3 proteins: Kininogen-1 heavy chain (21 – 379), bradykinin (380-388), Kininogen-1 light chain (389-661).

Good luck.

Dear Xiaojing,

As you may know, most proteins are synthesized as “precursors” and undergo posttranslational processing (“maturation”) that may occur while translation is still continuing or after it is over. There are dozens of posttranslational modifications (e.g. phosphorylation, glycosylation, alkylation, etc.). For example, in eukaryotes, all protein synthesis starts with methionine, which is in many cases removed upon processing. Many precursors contain so called “signal” sequences that are also removed upon maturation. Protein databases (including NCBI) usually show sequences for unprocessed proteins (i.e.”precursors”) , many of which just don’t exist in “real life”. In order to find some information about posttranslational modifications for each individual protein, you may turn to UniProtKB database (Swiss Institute of Biotechnology; http://www.uniprot.org) which is one of the most comprehensive and manually annotated protein databases. You need to keep in mind, however, that beside well established modifications, they often mention some predicted ones (for example, modifications “by similarity”), and these latter not necessarily occur at all. In your particular case, kininogen-1 (what is the species? Let’s say, mouse protein): the precursor (661 residues) contains a signal 1-20, which is removed, then the rest (21-661) is cleaved into 3 proteins: Kininogen-1 heavy chain (21 – 379), bradykinin (380-388), Kininogen-1 light chain (389-661).

Good luck.

In addition to what Yakov Koen said, you also need to know how the database searching software works. It is going to pull up the best match to the obtained fragments, and report that. If only the precursor form of the protein is in the database, it will give you that based on the score, although your specific protein may be the processed (mature) form. To determine if you have a processed form or not, different methods will need to be used (e.g. time of flight mass spec, N-terminal sequencing).

In addition to what Richard Heath said, just a hint. Before you do any further experimental analyses, you may run simply an alignment (virtual) of the matching fragments against complete sequence of the matched protein using BLAST (http://web.expasy.org/blast) and see, which portion of the full sequence is covered by your matching peptides. This would not prove anything, because there might be peptides missing from your experimental data, but you may get a clue, especially in case of kininogen. Hope this will be of help.

Dear Yakov,

Thank you very much for your detailed answer. The species is mouse. I will turn to search SwissProt database. However, I am still confused with the expression form of the proteins, ie, what does "flags" mean? what does"contains" mean? Could you recommend me some book or journal article which tells how to understand the protein name, please? Thank you a lot.

Dear Richard,

Thank you for your kind help. Since I havent learnt how to use the software, I will have a try if I can handle the problem as your instruction.