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bioRxiv · 10.1101/496349

Detecting modifications in proteomics experiments with Param-Medic

May, D.·Tamura, K.·Noble, W.
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Abstract

Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling, tandem mass tags, and phosphorylation, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open source Python and C++ implementations in a new version of the software tool Param-Medic.

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May, D., Tamura, K., Noble, W.. 2018-12-14. Detecting modifications in proteomics experiments with Param-Medic. https://doi.org/10.1101/496349

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