Today, Waterloo software developers, Bioinformatics Solutions Inc. have launched their latest suite of proteomic software, PEAKS Studio 4.2. Among the preliminary benefits, de novo sequencing and protein identification, the latest advancements include faster processing time, simple reporting and improved exporting features. These are all provided in an attempt to reduce research time and increase accuracy. The software was released to the public following email notification of the upgrade to current customers. “Speed and efficiency were our goals for the new release,” says Iain Rogers. “Our focus has resulted in users being able to not only view their results quickly, but in the format and order they prefer.” An example is users can now view only publishable results: proteins identified by more than one high scoring peptides. Result reports can be filtered by a number of criteria (delta mass, proteins with X# of good hits inclusive and exclusive, etc). A simple report to summarize de novo sequencing on a whole run has been included. Further, the scans may now be sorted by scan number, mass, m/z, or retention time. The de novo options screen allows users to limit the number of variable modifications allowed in a proposed de novo sequence. In regards to exporting data to other locations PEAKS 4.2 allows use of spectra images, spectra with ions annotated, sequence-spectrum alignment, ion tables and error plots can now be exported in high resolution for printing. WYSIWYG (What You See Is What You Get) export of protein ID results, both from ‘peptide view’ and ‘protein view’ has been enabled. The embedded software, SPIDER, Software Protein Identifier, has been recalibrated for increased speed (several fold), along with accuracy. Perhaps the largest problem of the field of research is the multiple variations of file formats produced. In an attempt to create a uniform format, PEAKS supports HUPO’s (Human Proteome Organization) proposed file format standard: mzData. Preliminary testers are raving about the new appearance of PEAKS and that is generally a good sign of the success in Mr. Rogers’ focus into user coherence.