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Most lay people reading the results of a mass spectrometry peptide analysis, wouldn't make head nor tails of it, but with Randy Whittal it's a different story.

Used to poring over such data for hours and manually putting together the puzzle pieces that when completed, for Whittal the analysis would reveal a brand new biological structure.

Peptides, or small proteins, are a collection of amino acids, strung together to create life. Without these basic strings of biological matter that emerged from the Earth's primordial soup, humanity – and all life on Earth – simply wouldn't exist. It's no wonder that modern-day chemists are looking for the best tools available to help them understand these building blocks of life.

For Whittal, the director of mass spectrometry in the department of chemistry at the University of Alberta, a pencil and paper powered by his own brain was the best tool to do that. Until he found PEAKS software, powered by Waterloo, Ont.-based Bioinformatics Solutions Inc.

Done manually it's quite a time consuming process.

"You basically sit down with a calculator and a mass spectrum sitting in front of you,” he says. “It could take anywhere between 15 minutes and an hour for a spectrum. Of course, PEAKS comes up with the answer for you in a few seconds.”

The software that Whittal describes as the best he's ever used for peptide sequencing was invented by Bin Ma, founder of Bioinformatics Solutions and a professor at the University of Waterloo. Since its development, PEAKS has earned a place in the labs of pharmaceutical companies, government research facilities, and academic institutions around the world. It is known for its unparalleled accuracy in de novo sequencing – the process of identifying a completely new peptide that hasn't been encountered before.

Scientists typically rely on large databases of known peptides when trying to identify one they are studying. The peptides found in the human body, for example, are fairly well known. But the method can lead to errors when a new type of organism is being examined. A database stands no chance of identifying a brand new discovery – and neither does a human.

“Mass spectrometry generates a lot of data about the protein. No human can actually go through it all,” Ma says. “Using de novo sequencing is like having an infinitely large universal database with every possible sequence in it. We've made an algorithm to do this efficiently.”

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