Dataset Information

MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms.

ABSTRACT: Mass Spectrometry (MS)-based proteomics has become an essential tool in the study of proteins. With the advent of modern MS machines huge amounts of data is being generated, which can only be processed by novel algorithmic tools. However, in the absence of data benchmarks and ground truth datasets algorithmic integrity testing and reproducibility is a challenging problem. To this end, MaSS-Simulator has been presented, which is an easy to use simulator and can be configured to simulate MS/MS datasets for a wide variety of conditions with known ground truths. MaSS-Simulator offers many configuration options to allow the user a great degree of control over the test datasets, which can enable rigorous and large- scale testing of any proteomics algorithm. MaSS-Simulator is assessed by comparing its performance against experimentally generated spectra and spectra obtained from NIST collections of spectral library. The results show that MaSS-Simulator generated spectra match closely with real-spectra and have a relative-error distribution centered around 25%. In contrast, the theoretical spectra for same peptides have relative-error distribution centered around 150%. MaSS-Simulator will enable developers to specifically highlight the capabilities of their algorithms and provide a strong proof of any pitfalls they might face. Source code, executables, and a user manual for MaSS-Simulator can be downloaded from https://github.com/pcdslab/MaSS-Simulator.

SUBMITTER: Awan MG

PROVIDER: S-EPMC6400488 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms.

Awan Muaaz Gul MG Saeed Fahad F

Proteomics 20180928 20

Mass Spectrometry (MS)-based proteomics has become an essential tool in the study of proteins. With the advent of modern MS machines huge amounts of data is being generated, which can only be processed by novel algorithmic tools. However, in the absence of data benchmarks and ground truth datasets algorithmic integrity testing and reproducibility is a challenging problem. To this end, MaSS-Simulator has been presented, which is an easy to use simulator and can be configured to simulate MS/MS dat ...[more]

PMID: 30216669

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Project description:BACKGROUND: Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. RESULTS: In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). CONCLUSIONS: We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CeMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http://maltcms.sf.net. The evaluation scripts of the present study are available from the same source.

Dataset Information

MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms.

Publications

MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms.

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