Dataset Information

Significance estimation for large scale metabolomics annotations by spectral matching.

ABSTRACT: The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate (FDR) for 70 public metabolomics data sets. We show that the spectral matching settings need to be adjusted for each project. By adjusting the scoring parameters and thresholds, the number of annotations rose, on average, by +139% (ranging from -92 up to +5705%) when compared with a default parameter set available at GNPS. The FDR estimation methods presented will enable a user to assess the scoring criteria for large scale analysis of mass spectrometry based metabolomics data that has been essential in the advancement of proteomics, transcriptomics, and genomics science.

SUBMITTER: Scheubert K

PROVIDER: S-EPMC5684233 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Significance estimation for large scale metabolomics annotations by spectral matching.

Scheubert Kerstin K Hufsky Franziska F Petras Daniel D Wang Mingxun M Nothias Louis-Félix LF Dührkop Kai K Bandeira Nuno N Dorrestein Pieter C PC Böcker Sebastian S

Nature communications 20171114 1

The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate (FDR) for 70 public metabolomics data sets. We show that the spectral matching settings need to be adjusted f ...[more]

PMID: 29133785

Similar Datasets

Project description:BackgroundCardinality matching (CM), a novel matching technique, finds the largest matched sample meeting prespecified balance criteria thereby overcoming limitations of propensity score matching (PSM) associated with limited covariate overlap, which are especially pronounced in studies with small sample sizes. The current study proposes a framework for large-scale CM (LS-CM); and compares large-scale PSM (LS-PSM) and LS-CM in terms of post-match sample size, covariate balance and residual confounding at progressively smaller sample sizes.MethodsEvaluation of LS-PSM and LS-CM within a comparative cohort study of new users of angiotensin-converting enzyme inhibitor (ACEI) and thiazide or thiazide-like diuretic monotherapy identified from a U.S. insurance claims database. Candidate covariates included patient demographics, and all observed prior conditions, drug exposures and procedures. Propensity scores were calculated using LASSO regression, and candidate covariates with non-zero beta coefficients in the propensity model were defined as matching covariates for use in LS-CM. One-to-one matching was performed using progressively tighter parameter settings. Covariate balance was assessed using standardized mean differences. Hazard ratios for negative control outcomes perceived as unassociated with treatment (i.e., true hazard ratio of 1) were estimated using unconditional Cox models. Residual confounding was assessed using the expected systematic error of the empirical null distribution of negative control effect estimates compared to the ground truth. To simulate diverse research conditions, analyses were repeated within 10 %, 1 and 0.5 % subsample groups with increasingly limited covariate overlap.ResultsA total of 172,117 patients (ACEI: 129,078; thiazide: 43,039) met the study criteria. As compared to LS-PSM, LS-CM was associated with increased sample retention. Although LS-PSM achieved balance across all matching covariates within the full study population, substantial matching covariate imbalance was observed within the 1 and 0.5 % subsample groups. Meanwhile, LS-CM achieved matching covariate balance across all analyses. LS-PSM was associated with better candidate covariate balance within the full study population. Otherwise, both matching techniques achieved comparable candidate covariate balance and expected systematic error.ConclusionsLS-CM found the largest matched sample meeting prespecified balance criteria while achieving comparable candidate covariate balance and residual confounding. We recommend LS-CM as an alternative to LS-PSM in studies with small sample sizes or limited covariate overlap.

Dataset Information

Significance estimation for large scale metabolomics annotations by spectral matching.

Publications

Significance estimation for large scale metabolomics annotations by spectral matching.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets