The key challenge in aligning protein level results is flexible matching by making use of the accession ambiguity in reported protein groups. The better this task is done, the more complete will be the protein matching across multiple results. For quantitative work, a high degree of protein matching translates to a low degree of incomplete data in the protein feature table.

This Excel template uses the accession ambiguity preserved in the Pro Group Algorithm and aligns and compares protein-level results across multiple searches from ProteinPilot software. Up to 10 searches can be aligned at a time. The method used here is to align each individual search to a reference protein ID result (a MasterSearch), which is created by searching a tractable amount of the individual data into a single *.group result.

Identification results: One example of template use is for method development, one can compare the results from various methods (fractionation, acquisition, etc) and investigate the population of proteins found and the sequence coverage per protein found between the different methods.

Quantification results: Another use of this template is alignment of multiple label-based quantitation experiments. Using 8plex iTRAQ reagents, each search result produces 7 ratios vs a global internal standard (GIS) sample. This template handles 10 results at a time, which means that the quantitative results from up to 70 samples can be aligned in one use of this template.

Excel 2010 installed as a 64-bit application is recommended for handling this large processing-intensive Excel sheet. More information on requirements and limitations can be found in the Instructions tab in the template

For version and download information, see this link.