Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity

Silva, Ana Sílvia Ferreira Diamantino Coelho e; Palmer, Andrew; Kovalev, Vitaly; Тарасов, А. В.; Alexandrov, Theodore; Martens, Lennart; Degroeve, Sven

doi:10.1021/acs.analchem.8b03224

Cited by 8 publications

(10 citation statements)

References 15 publications

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“…Analysis of the tandem mass spectrometry data was performed using Ionbot (unpublished, based on the work of Silva et al 65 , https://ionbot.cloud), a sequence database search tool based on machine learning capable of performing rapid open modification and open mutation searches. Ionbot was used under a beta-tester version supplied by Sven Degroeve and Lennart Martens (Ghent University, VIB).…”

Section: Mass Spectrometry Validationmentioning

confidence: 99%

The RNA Atlas expands the catalog of human non-coding RNAs

et al. 2021

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Existing compendia of non-coding RNA (ncRNA) are incomplete, in part because they are derived almost exclusively from small and polyadenylated RNAs. Here we present a more comprehensive atlas of the human transcriptome, which includes small and polyA RNA as well as total RNA from 300 human tissues and cell lines. We report thousands of previously uncharacterized RNAs, increasing the number of documented ncRNAs by approximately 8%. To infer functional regulation by known and newly characterized ncRNAs, we exploited pre-mRNA abundance estimates from total RNA sequencing, revealing 316 microRNAs and 3,310 long non-coding RNAs with multiple lines of evidence for roles in regulating protein-coding genes and pathways. Our study both refines and expands the current catalog of human ncRNAs and their regulatory interactions. All data, analyses and results are available for download and interrogation in the R2 web portal, serving as a basis for future exploration of RNA biology and function.

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Section: Mass Spectrometry Validationmentioning

confidence: 99%

The RNA Atlas expands the catalog of human non-coding RNAs

et al. 2021

View full text Add to dashboard Cite

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“…Analysis of the tandem mass spectrometry data is performed using Ionbot (unpublished, based on the work of C Silva et al 52 , https://ionbot.cloud), a sequence database search tool based on machine learning capable of performing rapid open modification and open mutation searches. Ionbot was used under a beta-tester version supplied by Sven Degroeve and Lennart Martens (Ghent University, VIB).…”

Section: Methodsmentioning

confidence: 99%

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Lorenzi

Chiu

Cobos

et al. 2019

Preprint

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The human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines. We report on thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addition, we exploit intron abundance estimates from total RNA-sequencing to test and verify functional regulation by novel non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data, analyses, and results are available in the R2 web portal and serve as a basis to further explore RNA biology and function.

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“…Percolator has also been adopted for applications that it was not originally intended for. For example, it was adapted for use for the annotation of metabolites in imaging mass spectrometry, 22 grouping of MS1-features in label-free quantification, 27 and with the OpenSWATH pipeline for the analysis of data generated using data-independent acquisition. In these settings, the number of features associated with each data point can be quite large.…”

Section: Motivationmentioning

confidence: 99%

Speeding Up Percolator

et al. 2019

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The processing of peptide tandem mass spectrometry data involves matching observed spectra against a sequence database. The ranking and calibration of these peptide-spectrum matches can be improved substantially using a machine learning postprocessor. Here, we describe our efforts to speed up one widely used postprocessor, Percolator. The improved software is dramatically faster than the previous version of Percolator, even when using relatively few processors. We tested the new version of Percolator on a data set containing over 215 million spectra and recorded an overall reduction to 23% of the running time as compared to the unoptimized code. We also show that the memory footprint required by these speedups is modest relative to that of the original version of Percolator.

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Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity

Cited by 8 publications

References 15 publications

The RNA Atlas expands the catalog of human non-coding RNAs

The RNA Atlas expands the catalog of human non-coding RNAs

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Speeding Up Percolator

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