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Posted by Ville Koskinen (July 20, 2022)

Does your search engine show the evidence?

You’ve submitted a protein sequence database search and start looking at the results. Why did the search engine identify that protein? What is the peptide evidence? Which alternatives did the software consider? Is the software’s decision correct? These are basic yet important questions with any software-driven approach – which is the bulk of today’s MS/MS data analysis. A lot of [...]

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Posted by Ville Koskinen (October 14, 2019)

Is your database search reproducible?

A lot has been written about the reproducibility of shotgun proteomics workflows, as well as controlling measurement variability between instruments and laboratories. An equally important factor is data analysis transparency and reproducibility, which is gaining increasing visibility. This boils down to two essentials: recording all software parameters used, and ensuring the software produces the same output given the same input [...]

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