"iD-plus" MS-based search engine for protein identification

Copyright© 2017-2020,IPR Osaka Univ.

Metastable decomposition at the peptide C‐terminus: Possible use in protein identification
                                                                 Rapid Communications in Mass Spectrometry    07 February 2020

Using iD-plus

1.Search parameter reference
The Taxonomy parameter allows searches to be limited to entries from particular species or groups of species. This can speed up a search, and ensures that the hit list will only contain entries from the selected species. If the search data are marginal, and you are completely confident of the origin of the protein, this can help bring a weak match to the top of the list.
Select any known or suspected modifications on Cys residue.
Missed Cleavages
Setting the number of allowed missed cleavage sites to zero simulates a set of peptides perfectly digested.
If the digest mixture contains some partially digested peptides, you may choose a setting of 1, or maybe 2 missed cleavage sites.
The error window on experimental peptide mass values, the absolute unit is Da.
Query (m/z, C-term AA)
The frame to input data.
Press the button “Run” to run the database searching.
Press the button “Demo” to run a demo database searching program. A series of demo data will be added into the Query frame, and press the button “Run demo” to produce a summary report in the .csv format.
2.Data file format
iD-plus Generic Format
The iD-plus generic format for a data file submitted to iD-plus is (square brackets indicate optional elements, they should not be included in an actual data file):
Query 1
Query 2
Query N
In iD-plus,each query is a combination of a peptide m/z value and a 1-letter abbreviation of amino acid on the C-terminal of the peptide. For example:

In some cases, “B” represents either lysine or glutamine, and "J" either leucine or isoleucine.
3.Result report overview
At the completion of a search, a summary report is produced as a .csv document and could be saved at any location in the PC.
The protein coverage of identified peptides, protein ID, mass value of peptides and their sequence would be listed in the report.
Coverage (%)
The percentage of the lengths of the identified peptides occupied in the whole length of the candidate protein.
The ID of the candidate protein in protein database (SwissProt).
peptide1, 2, …
The information of the identified peptides, including m/z values and amino acid sequences. The double quotes " indicates the content is same as the above cell.
Taxonomy, Cys(-SR), allow up to n miss cleavage, Error
Please refer to the explanations in Part 1 Search parameter reference.
Obs. m/z, c-term
Please refer to the explanations in Part 2 Data file format.
The asterisk * indicates the corresponding query which represents an identified peptide.

A description of the output file of the Demo is shown as follows: