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Articles tagged: mzIdentML

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Posted by Ville Koskinen (May 20, 2022)

mzIdentML 1.2

Mascot Server supports several formats for exporting database search results. One of them is the Proteomics Standards Initiative’s mzIdentML. The Mascot 2.8.1 patch release upgrades the file format version to mzIdentML 1.2. You can now export crosslinked search results in XML, CSV, xiVIEW CSV and mzIdentML format. When you export standard database searches, error tolerant searches and spectral library searches, [...]

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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 (August 15, 2015)

PSI file formats, part 3: repositories

We’ve talked about mzIdentML validity only in terms of file structure. Proteomics repositories, such as PRIDE or ProteoRed, of course require files to be valid in that sense, but they impose additional requirements. If you need to upload your search results to a repository, it is worth looking at this more extended idea of validity. For simplicity, I’ll only consider [...]

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Posted by Ville Koskinen (June 17, 2015)

PSI file formats, part 2: validation

The first part listed a number of ways for generating mzIdentML files and named a few pieces of software capable of reading and processing them. This part of the series discusses a rather technical issue with mzIdentML files, namely validity, and how it can affect you as a user. Validation is somewhat tangled with submitting mzIdentML files to proteomics repositories, [...]

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Posted by Ville Koskinen (May 14, 2015)

PSI file formats, part 1: mzIdentML

Mascot search results are saved in a .dat format, which contains all protein and peptide identifications output by Mascot, as well as auxiliary information (search parameters, mass definitions for modifications, etc.). The .dat file is almost never the final step in data analysis; for the next step, you need to import the search results in some other piece of software. [...]

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