New web site features, September 2001

ICAT support

Isotope-Coded Affinity Tag (ICAT) is a method for protein quantitation developed by Gygi and co-workers. The cysteine residues of proteins from one cell state are derivatised with an isotopically light (d0) biotin affinity tag. Proteins from a second cell state are derivatised with an isotopically heavy (d8) tag. The proteins are pooled, digested, and the tagged peptides isolated by affinity chromatography. When analysed by mass spectrometry, quantitative information is provided by the ratio between the light and heavy signal intensities for each peptide.

In Mascot, ticking the ICAT box limits the search to cysteine containing peptides, (equivalent to a comp(*[C]) term). It also adds heavy and light ICAT tags to the list of variable modifications. The default ICAT masses correspond to the ICAT kit distributed by Applied Biosystems.

UniGene clustering of dbEST matches

One of the drawbacks of searching dbEST is that there are very few long sequences, so that extended groupings of peptide matches into protein matches are rare. This can be rectified with UniGene, an index created by automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster is a list of the GenBank sequences, including EST’s, which represent a unique gene. It is not an attempt to produce a consensus sequence.

You will find links to generate species based UniGene reports just above the "Repeat Search" buttons on the Peptide Summary report from any dbEST search. Following a Protein View link from a UniGene report will display a list of Unigene family members in place of the standard Protein View.

Other important changes

  • More accurate taxonomy for NCBI databases
  • In the results report from a peptide mass fingerprint search, there is now an option to repeat the search using just the mass values which were unmatched in the top hit.
  • Protein View contains new links for the unformatted sequence string and the pI value.
  • The fragment ion table in Peptide View now runs down the page, rather than across, to make printing easier.
  • Mass error graphs are included in Protein View and Peptide View
  • Neutral loss from fragment ions containing phosphorylated serine and threonine is now handled correctly