Information Flow
                   Data Definitions
                                  Functionalities
                                                Curation Protocol
                                                                     Export Data



The Information Flow implemented in the application
is shown schematically in the following Figure:


click on the image to enlarge

The Data Definitions and Relations used in the application

are shown schematically in the following Figure:


click on the image to enlarge

Summary of Functionalities:
There are 3 modes of searching available:

|1|
Search whether or not a given molecular mass or a list of molecular masses can be found exclusively in one Human protein, i.e. is a UMM

The system answers whether or not each submitted mass can be found exclusively in a human protein and provides the user with the corresponding peptide and protein as well as the corresponding smallest range (IR) where no other molecular mass can be measured in Human Proteome. Upon user request, when at least one unique mass from the given list has been found, the system provides the user with the masses from the given list that are not unique but  can be measured in the corresponding protein(s).

|2|
Search whether or not a given peptide sequence or a list of peptide sequences can be found exclusively in one Human protein, i.e. is a UP or a CUP

The system answers whether or not each peptide sequence is a core unique peptide sequence (CUP) or whether it contains or belongs to a core unique peptide sequence. In case that a peptide sequence is found to be a CUP, the user is provided with the corresponding peptide mass, protein, and “container”-peptide sequence that can be found through enzymatic digestion. Additionally, upon user request, the peptide sequence can potentially be further investigated for uniqueness across all species in the Swiss-Prot. If a given sequence is not among the CUPs, it is digested into subsequences in order to investigate whetehr or not a subsequence of the initial sequence is a CUP. If it is, then the given sequence is a UP but not a CUP. If it is not, the given sequence is matched to the set of CUPs to investigate whether or not it is a part of a larger sequence characterized as a CUP. In case of a positive match, the given sequence is a fragment of one or more CUPs. In a different case, the given sequence is definitely not unique in Humans.

|3|
Search, given a specific protein, whether or not unique molecular masses or unique peptide sequences exist
The system provides the user with a list of UMMs with their corresponding peptide sequences as well as with a list of CUPs and their corresponding molecular masses. The user can also find which unique protein fragments can computationally derive from a set of enzymes.
Curation Protocol:
The DataBase and File Repository used by UniMaP are updated on a periodical manner, using proper perl scripts. The updating procedure is described in the following scheme:



The UniMaP database and file repository are at least updated
at each major release of the Swiss-Prot Database.

Current Version:
The current version of Swiss-Prot used to compile our data is the major release:
 UniprotKB release 15, Swiss-Prot 57

Export Data:

To facilitate the export of data, there is a link near each result table named
"View and Download Table".

When the user clicks the above link, a new page with tabulated results is shown.
The user has to select on her/his browser: File ->Save Page As
and put a proper name with file extention ".xls"

Then an excel file is created with properly tabulated the info shown on the page.