Refinements of LC-MS/MS Spectral Counting Statistics Improve Quantification of Low Abundance Proteins View Full Text


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Article Info

DATE

2019-09-20

AUTHORS

Ha Yun Lee, Eunhee G. Kim, Hye Ryeon Jung, Jin Woo Jung, Han Byeol Kim, Jin Won Cho, Kristine M. Kim, Eugene C. Yi

ABSTRACT

Mass spectrometry-based spectral count has been a common choice of label-free proteome quantification due to the simplicity for the sample preparation and data generation. The discriminatory nature of spectral count in the MS data-dependent acquisition, however, inherently introduces the spectral count variation for low-abundance proteins in multiplicative LC-MS/MS analysis, which hampers sensitive proteome quantification. As many low-abundance proteins play important roles in cellular processes, deducing low-abundance proteins in a quantitatively reliable manner greatly expands the depth of biological insights. Here, we implemented the Moment Adjusted Imputation error model in the spectral count refinement as a post PLGEM-STN for improving sensitivity for quantitation of low-abundance proteins by reducing spectral count variability. The statistical framework, automated spectral count refinement by integrating the two statistical tools, was tested with LC-MS/MS datasets of MDA-MB468 breast cancer cells grown under normal and glucose deprivation conditions. We identified about 30% more quantifiable proteins that were found to be low-abundance proteins, which were initially filtered out by the PLGEM-STN analysis. This newly developed statistical framework provides a reliable abundance measurement of low-abundance proteins in the spectral count-based label-free proteome quantification and enabled us to detect low-abundance proteins that could be functionally important in cellular processes. More... »

PAGES

13653

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-019-49665-1

DOI

http://dx.doi.org/10.1038/s41598-019-49665-1

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1121115995

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/31541118


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