UniQua: A Universal Signal Processor for MS-Based Qualitative and Quantitative Proteomics Applications

Recent developments in high resolution mass spectrometry
(HR-MS)
technology have ushered proteomics into a new era. However, the importance
of using a common, open data platform for signal processing of HR-MS
spectra has not been sufficiently addressed. In this study, a MS signal
processor was developed to facilitate data integration from different
instruments and different proteomics approaches into a unified platform
without compromising protein identification and quantitation performance.
This processor supports parallel processing capability which allows
full utilization of computing resources to speed up signal processing
performance to >1 gigabytes/min. The storage space occupied by
the
processed MS data can be reduced to ∼10%, which helps the analysis
and management of large quantities of data from comprehensive proteomics
studies. For quantitation at the MS level, processing accuracy is
improved and processing time for ASAPRatio is reduced to ∼50%.
For quantitation at the MS/MS level, accurate reporter ion ratios
from different instruments can be directly determined by the processed
MS/MS spectra and reported in the Mascot search result directly without
using specialized iTRAQ software.