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Posted by Ville Koskinen (April 14, 2020)

Human Proteome Project data interpretation guidelines

The Human Proteome Project (HPP) data interpretation guidelines were recently updated. Many of the guidelines are good practice and common sense in any proteomics study where reliable protein identification is critical, not just when studying the human proteome. The guidelines are easy to meet using Mascot Server 2.7. Core guidelines The full list consists of 9 guidelines. The first one [...]

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Posted by Ville Koskinen (August 12, 2017)

Exporting spectral library search results

Mascot 2.6 integrates spectral library searching. Today we’ll describe how these searches can be exported. Please ensure you’ve installed the Mascot 2.6.1 patch, as support for exporting library search data was not complete in the initial Mascot 2.6.0 release. Library searches can be either library-only or integrated searches. Integrated means the search is against both a spectral library and a [...]

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Posted by Ville Koskinen (October 21, 2015)

PSI file formats, part 4: mzTab

mzTab is a relatively new file format for reporting protein and peptide search results. Its specification (1.0) was published in June 2014. Like mzIdentML, it is developed by the Proteomics Standards Initiative (PSI) and shares some of the same controlled vocabulary (CV). However, that’s where the similarities end. The biggest differences are that mzTab is table-based text, not XML, and [...]

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