TY - JOUR
T1 - Statistical detection of differentially abundant ions in mass spectrometry-based imaging experiments with complex designs
AU - Bemis, Kylie A.
AU - Guo, Dan
AU - Harry, April J.
AU - Thomas, Mathew
AU - Lanekoff, Ingela
AU - Stenzel-Poore, Mary P.
AU - Stevens, Susan L.
AU - Laskin, Julia
AU - Vitek, Olga
N1 - Funding Information:
We thank Allison Dill and R. Graham Cooks of Purdue University for providing access to the Renal Cell Carcinoma experiment. This work was supported by NSF CAREER award DBI-1054826 to O.V, and by funds VR 621-2013-4231 and SSF ICA-6 to I.L. J.L. and M.T. acknowledge support from grant ES024229-01 from the National Institute of Environmental Health Sciences (NIEHS). Part of this research was performed in EMSL, a national scientific user facility sponsored by the DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL) in Richland, WA. PNNL is a multi-program national laboratory operated by Battelle for the DOE under contract DE-AC05-76RLO 1830.
Funding Information:
We thank Allison Dill and R. Graham Cooks of Purdue University for providing access to the Renal Cell Carcinoma experiment. This work was supported by NSF CAREER award DBI-1054826 to O.V, and by funds VR 621-2013-4231 and SSF ICA-6 to I.L. J.L. and M.T. acknowledge support from grant ES024229-01 from the National Institute of Environmental Health Sciences (NIEHS) . Part of this research was performed in EMSL, a national scientific user facility sponsored by the DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL) in Richland, WA. PNNL is a multi-program national laboratory operated by Battelle for the DOE under contract DE-AC05-76RLO 1830.
Publisher Copyright:
© 2018 Elsevier B.V.
PY - 2019/3
Y1 - 2019/3
N2 - Mass Spectrometry Imaging (MSI) characterizes changes in chemical composition between regions of biological samples such as tissues. One goal of statistical analysis of MSI experiments is class comparison, i.e. determining analytes that change in abundance between conditions more systematically than as expected by random variation. To reach accurate and reproducible conclusions, statistical analysis must appropriately reflect the initial research question, the design of the MSI experiment, and all the associated sources of variation. This manuscript highlights the importance of following these general statistical principles. Using the example of two case studies with complex experimental designs, and with different strategies of data acquisition, we demonstrate the extent to which choices made at key points of this workflow impact the results, and provide suggestions for appropriate design and analysis of MSI experiments that aim at detecting differentially abundant analytes.
AB - Mass Spectrometry Imaging (MSI) characterizes changes in chemical composition between regions of biological samples such as tissues. One goal of statistical analysis of MSI experiments is class comparison, i.e. determining analytes that change in abundance between conditions more systematically than as expected by random variation. To reach accurate and reproducible conclusions, statistical analysis must appropriately reflect the initial research question, the design of the MSI experiment, and all the associated sources of variation. This manuscript highlights the importance of following these general statistical principles. Using the example of two case studies with complex experimental designs, and with different strategies of data acquisition, we demonstrate the extent to which choices made at key points of this workflow impact the results, and provide suggestions for appropriate design and analysis of MSI experiments that aim at detecting differentially abundant analytes.
KW - DESI MSI
KW - Experimental design
KW - Mass spectrometry imaging
KW - Nano-DESI MSI
KW - Spatial statistics
KW - Statistical analysis
UR - http://www.scopus.com/inward/record.url?scp=85052079505&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85052079505&partnerID=8YFLogxK
U2 - 10.1016/j.ijms.2018.07.006
DO - 10.1016/j.ijms.2018.07.006
M3 - Article
AN - SCOPUS:85052079505
SN - 1387-3806
VL - 437
SP - 49
EP - 57
JO - International Journal of Mass Spectrometry
JF - International Journal of Mass Spectrometry
ER -