Select the protein database to be searched. The databases available on emPAI Calc are:
|IPI_Human||International Protein Index||http://www.ebi.ac.uk/IPI/IPIhelp.html|
|Ecoli SwissProt||High quality, curated protein database||http://au.expasy.org/sprot/|
|yeast_orf||Saccharomyces Genome Database (SGD)||http://www.yeastgenome.org/|
|Ecoli_MoriLab||GenoBase (Escherichia coli K12 W3110)||http://ecoli.naist.jp/|
|Arabidopsis_tair||The Arabidopsis Information Resource (TAIR)||http://www.arabidopsis.org/|
We can add new protein database by FASTA files upon request. [Contact]
|Shinoda, K. et al. (2006)||C18||(A) water and (B) acetonitrile , both with 0.2% formic acid|| linear gradient
(B) 1%-40% (0-50 min)
(B) 40%-50% (50-55 min)
|Ishihama, Y. (2005)||C18||(A) 0.5 acetic acid
(B) 0.5% acetic acid, 80% acetonitrile
|(B) 5%-60% (0-180 min)|||
|Krokhin, O. V. et al. (2004)||C18||Water and acetonitrile, with 0.1% TFA||A linear gradient of 1-80% acetonitrile in 60 min|||
|Petritis, K. et al. (2003)||Fused silica capillary columns packed with 5-um C18 particles ||(A) acetic acid/TFA/water (0.2:0.05:100 v/v)
(B) TFA/acetonitrile/water (0.1:90:10, v/v)
|nonlinear (exponential) gradient ||[4,6]|
|Bold / light||The first time a peptide match to a query appears in the report, it is shown in bold face.|
|Red / Black||Black peptide is second (or below) ranked candidate assigned to a MS/MS peak. Whenever the top ranking peptide match appears, it is shown in red.|
|Checked / Unchecked||It is not always clear which peptide "belongs" to which protein. "Checked" peptide means that the peak is also assigned to other protein(s) as "black" peptide.|
Description for "score" and "identity threshold"
from Matrix Science website
In Mascot, the score for an MS/MS match is based on the absolute probability (P) that the observed match between the experimental data and the database sequence is a random event. The reported score is -10Log(P). So, during a search, if 1.5 x 10^5 peptides fell within the mass tolerance window about the precursor mass, and the significance threshold was chosen to be 0.05, (a 1 in 20 chance of a false positive), this would translate into a score threshold of 65.
If the quality of an MS/MS spectrum is poor, particularly if the signal to noise ratio is low, a match to the "correct" sequence might not exceed this absolute threshold. Even so, the match to the correct sequence could have a relatively high score, which is well differentiated from the quasi-normal distribution of 1.5 x 10^5 random scores. In other words, the score is an outlier. This would indicate that the match is not a random event and, on inspection, such matches are often found to be either the correct match or a match to a close homologue. For this reason, Mascot also attempts to characterise the distribution of random scores, and provide a second, lower threshold to highlight the presence of any outlier. The lower, relative threshold is reported as the "homology" threshold while the higher, absolute threshold is reported as the "identity threshold".