CPTAC Studies 1 and 5: dissecting variability in multi-site LC-MS/MS proteomics through quality metrics and robust hierarchical multivariate statistics

Published

February 4, 2014

Author(s)

Stephen E. Stein, David M. Bunk, Xia Wang, Matthew Chambers, Lorenzo J. Vega-Montoto, David L. Tabb

Abstract

Shotgun proteomics experiments integrate a complex sequence of processes, any of which can introduce variability. Quality metrics computed from LC-MS/MS data have relied upon identifying MS/MS scans, but a new mode for the QuaMeter software produces metrics that are independent of identifications. Rather than evaluating each metric independently, we have created a robust multivariate statistical toolkit that accommodates the correlation structure of these metrics and allows for hierarchical relationships among data sets. The framework enables visualization and structural assessment of variability. Study 1 for the Clinical Proteomics Technology Assessment for Cancer (CPTAC), which analyzed three replicates of two common samples at each of two time points among 23 mass spectrometers in nine laboratories, provided the data to demonstrate this framework, and CPTAC Study 5 provided data from complex lysates to complement these findings. Identification-independent quality metrics enabled the differentiation of sites and run-times through robust principal components analysis and subsequent factor analysis. Dissimilarity metrics revealed outliers in performance, and a nested ANOVA model revealed the extent to which all metrics or individual metrics were impacted by mass spectrometer and run time. Study 5 data revealed that even when SOPs have been applied, instrument-dependent variability remains prominent, although it may be reduced, while within-site variability is reduced significantly. Finally, identification-independent quality metrics were shown to be predictive of identification sensitivity in these data sets. QuaMeter and the associated multivariate framework are available from http://fenchurch.mc.vanderbilt.edu and http://homepages.uc.edu/~wang2x7/, respectively.

Citation

ACS Journal of Proteome Research

Volume

86

Pub Type

Journals

Download Paper

DOI Link

Keywords

proteomics, metrics

Citation

Stein, S. , Bunk, D. , Wang, X. , Chambers, M. , J., L. and Tabb, D. (2014), CPTAC Studies 1 and 5: dissecting variability in multi-site LC-MS/MS proteomics through quality metrics and robust hierarchical multivariate statistics, ACS Journal of Proteome Research, [online], https://doi.org/10.1021/ac4034455 | (Accessed April 20, 2024)