MGE-PortalWiki/EMOWSE

Information about MOWSE

Mowseparameters

You must supply various parameters in order to run Mowse successfully. We have provided default values for some of these parameters; information to help you can be found here.

Databases

We offer several databases for zour mowsesearch:

1. Domo

2. Prodom

3. Trembl

4. Sprot

5. Tremblnew

Enzymes

Use this to specify the reagent used for your protein digestion. Mowse currently supports the following reagents:

Reagents	Cleavage rule
Trypsin	C-term to K/R
Lys-C	C-term to K
Arg-C	C-term to R
Asp-N	N-term to D
V8-bicarb	C-term to E
V8-phosph	C-term to E/D
Chymotrypsin	C-term to F/W/Y/L/M
C N Br	C-term to M

Note that cleavage is not allowed if the following residue is proline and that Mowse automatically calculates for nearest-neighbour partial cleavages.

Error Tolerance

This specifies the error allowed for the accuracy of the experimental mass determinations.

Molecular weight

Use this to specify the (experimental) molecular weight of the entire protein. If you don't know this (or don't want to use this), specify 0. Mowse will then perform a search of all entries in the database.

Filter

If a total molecular weight was given, Mowse will restrict its search to a proteins with that total molecular weight +/- this percentage. A value of 25 is suggested for initial searches, which can be progressively widened for subsequent search attempts if no matches are found. Discrimination is best when the filter percentage is narrow, but some Mw estimates (particularly from SDS gels) should be given considerable allowance for error.

Partial Factors

This specifies the weighting given to partially-cleaved peptide fragments, with a range from 0.1 to 1.0. The factor effectively down-weights the score awarded to a partial fragment by the specified amount. For example, a Pfactor of 0.25 will reduce the score of partial fragments to 25% (one quarter) of the score of a complete ('perfect') peptide cleavage fragment of equal mass.

Computing all possible nearest-neighbour partial fragments adds significantly to the number of peptides entered in the database (by a factor of two). The major effect of this is to increase the background score by increasing the number of random Mw matches, which can significantly reduce discrimination. The use of a low Pfactor (eg 0.1 - 0.3) is a useful way of limiting this effect - partial peptide matches will add a little to the cumulative frequency score, but without compromising discrimination.

More experienced users can utilise the Pfactor to optimize searches where the peptide Mw data contain a significant proportion of partial cleavage fragments (eg > 30%). In such cases, setting the Pfactor within the range 0.4 - 0.6 can help to improve discrimination. Conversely, if the digestion is perfect, with no partial fragments present, the lowest Pfactor of 0.1 will give maximum discrimination.