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Articles tagged: PSI
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, [...]
Don’t wait: use spectral libraries now
The Human Proteome Project 2018 special issue in the Journal of Proteome Research contains a report from the 2017 Dagstuhl Seminar on Computational Proteomics. The paper by Deutsch et al. is titled Expanding the Use of Spectral Libraries in Proteomics, and the authors identify several challenges that slow down spectral library adoption. I’d like to address their main points. Adoption [...]
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 [...]
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 [...]
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, [...]
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. [...]