msprepCOPD: Example of processed mass spectrometry dataset

Description Usage Format Source References Examples


Data contains LC-MS metabolite analysis for samples from 20 subjects. and 662 metabolites. The raw data was pre-processed using MSPrep method. The raw data pre- processing include 3 steps- Filtering, Missing Value Imputation and Normalization. Filtering- the metabolites(columns) in the raw data were removed if they were missing more than 80 percent of the samples. Missing Value Imputation- The Bayesian Principal Component Analysis (BPCA) was applied to impute the missing values. Normalization- median normalization was applied to remove unwanted variation appears from various sources in metabolomics studies. The first three columns indicate "Mass" indicating the mass-to-charge ratio, "Retention.Time", and "Compound.Name" for each present metabolite. The remaining columns indicate abundance for each of the 645 mass/retention-time combination for each subject combination.




SummarizedExperiment assay object containing 645 metabolites (features) of 20 subjects (samples).


Mass-to-charge ratio




Compound name for each mass/retention time combination


The columns indicate metabolite abundances found in each subject combination. Each column begins with an 'X', followed by the subject ID.


The raw data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000438. The raw data can be accessed directly via it's Project DOI: 10.21228/M8FC7C This work is supported by NIH grant, U2C- DK119886.


Nichole Reisdorph. Untargeted LC-MS metabolomics analysis of human COPD plasma, HILIC & C18, metabolomics_workbench, V1.

Hughes, G., Cruickshank-Quinn, C., Reisdorph, R., Lutz, S., Petrache, I., Reisdorph, N., Bowler, R. and Kechris, K., 2014. MSPrep—Summarization, normalization and diagnostics for processing of mass spectrometry–based metabolomic data. Bioinformatics, 30(1), pp.133-134.



marr documentation built on March 10, 2021, 2 a.m.