msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies
作者： Berend Hoekman , Rainer Breitling , Frank Suits , Rainer Bischoff , Peter Horvatovich
关键词:
摘要: Data processing forms an integral part of biomarker discovery and contributes significantly to the ultimate result. To compare evaluate various publicly available open source label-free data workflows, we developed msCompare, a modular framework that allows arbitrary combination different feature detection/quantification alignment/matching algorithms in conjunction with novel scoring method their overall performance. We used msCompare assess performance workflows built from modules packages such as SuperHirn, OpenMS, MZmine our in-house on peptide-spiked urine trypsin-digested cerebrospinal fluid (CSF) samples. found quality results varied greatly among interestingly, heterogeneous combinations often performed better than homogenous workflows. Our showed union matrices outperformed original some cases. is software (https://trac.nbic.nl/mscompare), provide web-based service for by integration into Galaxy server Netherlands Bioinformatics Center (http://galaxy.nbic.nl/galaxy) allow scientists determine which provides most accurate particular LC-MS sets.
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