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Posted by Ville Koskinen (February 21, 2019)

X!Hunter MGF libraries

Mascot 2.6 supports three file formats for spectral libraries: the NIST MSP format, the SpectraST sptxt format and the X!Hunter MGF format. The sptxt format is a variation on MSP and will be covered in a future blog post. The main functional difference between MSP and MGF is in the level of annotation. The X!Hunter MGF format is minimalistic and [...]

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Posted by Ville Koskinen (December 17, 2018)

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 [...]

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Posted by John Cottrell (September 12, 2017)

How to create a spectral library for contaminants

An earlier article highlighted how modified and non-specific peptides from contaminants can be matched using a spectral library without increasing the search space for the target proteins. This is particularly useful for sequencing grade trypsin, which is modified by methylation or acetylation of the lysines, creating a large number of modified non-specific peptides that are missed by typical search strategies. [...]

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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 (July 12, 2017)

The most analysed protein is …

Trypsin, of course. The Journal of Proteome Research has a paper from the Medical University of Graz concerning the importance of correctly identifying spectra from contaminant proteins. In particular, trypsin autolysis peptides. The authors point out that sequencing grade trypsin is modified by methylation or acetylation of the lysines, to inhibit autolysis. Unless these variable modifications are selected in a [...]

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Posted by John Cottrell (December 13, 2016)

Protein inference for spectral library searches

The major new feature of Mascot Server 2.6, now running on this web site, is that searches of spectral libraries have been fully integrated with ‘conventional’ Mascot searches of Fasta files. The search engine for spectral library searches is MSPepSearch from Steve Stein and colleagues at NIST. We didn’t have any revolutionary ideas for improving spectral library scoring so, rather [...]

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