New release 4/19/2007

[robos...@gmail.com]

Some significant changes in this release:

- Scoring of prefix residue masses (PRMs), of tags, and of matches has
been improved. The F-score (weighted sum of Match Quality Score and
Delta-Score) is now included in the final output file.

- Tag generation now integrates flanking amino acid effects (e.g. if a
tag contains a proline, then the peaks on the N-terminal side should
be much stronger than those on the C-terminal side!)

- The XML parse engine, expat, is now used for mzXML and mzData
parsing. This should improve data handling (e.g. mzData files with
different peak precision levels).

- The PTMFinder algorithm for identifying valid PTM sites within
unrestrictive search results is now released as PTMAnalysis.py. (A
paper describing the algorithm in detail is in preparation)

UPGRADE NOTE: Because of improvements in scoring, MQScores from
previous versions and this version are not directly comparable. In
addition, note that the tab-delimited format of raw Inspect output has
changed slightly. (Tools using the ResultsParser class to read
annotations are unaffected)

In addition, the UCSD proteomics website is now at the prototype
stage. It will provide an easy-to-use interface for Inspect,
alongside other cutting-edge proteomics tools such as PepNovo. Watch
for a post within the next month announcing a publicly-accessible beta
version.