I just got a list of proteins from protein identification report and I would like to know, what is the minimum protein ID score obtained after protein identification that has to be cut off (where I can find references for that)? For my protein ID scores, most of them are below 30. How I can choose the reliable proteins?
What is the search engine used for the data analysis? The scores are very different and depend on the software used
in any case, you can always use the number of peptides identified per protein, the more peptides, the more confident your identification is
The analyzed MS/MS data from DeCyderMS were submitted for a database search using the Mascot software. The data was searched against the NCBI database for protein identification
Hi Lucky,
you can start with this publication:
http://www.ncbi.nlm.nih.gov/pubmed/10612281
This tutorial might also be useful:
http://www.ncbi.nlm.nih.gov/pubmed/21635977
Matrix Science has also a lot of documentation (www.matrixscience.com) about their MASCOT search engine.
A score of less than 30 in Mascot is generally not considered outstanding. Depending on the peptide length, it may be ok or in some cases borderline. Among other things, this is a function of the size of the database and the quality of the spectra that you search. If you have more than one peptide per protein, your confidence in that protein ID should increase.
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