Articles tagged: export

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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 John Cottrell (February 15, 2017)

Exporting search results: tips and tricks

The Mascot Server export utility allows search results to be exported in a wide range of formats, together with the native result file and the MGF peak list. Exporting the result file can be useful if you need it for a third party application and don’t have file share access to the Mascot Server. Exporting the MGF might be useful [...]

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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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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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Posted by John Cottrell (January 19, 2015)

Creating a list of confidently identified proteins

This can be done very easily using Report Builder: Select the Decoy checkbox when submitting the search Open the result report as a Protein Family Summary Switch to the Report Builder tab Expand the decoy search section and set the peptide FDR to 1% Expand the filters section and set ‘Num of significant unique sequences’ > 1 Optionally, expand the [...]

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