Usage

The digesters available are the following (Xaa denotes any amino acid, i.e. cutting between Xaa-Cys means that the digester cuts before every Cysteine):

Turning on Deuterated indicates that the protein has been treated with heavy water and that all the exchangeable hydrogen atoms are now deuterium atoms, causing an increase in their molecular weight.

The masses are fragment masses (in Dalton) obtained when digesting the given protein with the given enzyme. They can be separated by spaces, commas, tabs or newlines as convenient, but no other extraneous characters.

Each request may contain more than one digestion. These multiple digestions will be understood to be on the same protein. So naturally, each digester name can appear only once.

An optional modifier aa=mass indicates that the weight of the amino acid aa is to be considered mass. Such modifications happen when proteins are preprocessed with reagents that may change some amino acids, hence changing the weights of the fragments. For the cases of digestion with CNBr or TrypsinCysModified, since it is known that cysteine is transformed into homoserine or homoserinelactone for CNBr and to aminoethylcysteine for the second, the modifications are done automatically and no change needs to be indicated.

ApproxMass can be used to indicate an approximation to the weight of the entire protein being searched. This optional value, which is easily obtainable from 2D gels, increases the precision of the search. It is recommended that whenever the weight is known, it be used.

SampleSize indicates the number of hits to be reported. By default, the top ranking 15 proteins or genes are reported.

The results of the search are reported as a table:

• The first column measures the quality of the match between the given weights and a protein sequence in the database. The higher the score, the better the match. The hits are listed in decreasing scoring order.
• The second column, identified by n, indicates the number of fragments that will result from the digestion of the found protein.
• The third column, identified with k, indicates the number of given weights which were successfully matched against the theoretical digestion. The score is calculated from the total number of fragments, the number of given weights matched, and from how closely these weights could be matched.
• The fourth column indicates the accession number of the sequence in SwissProt.
• The rest of each line contains the description and species of the sequence which serve as a quick guide to identify the protein.