ArticleProteomics2018
MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms.
Article in Proteomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra.Bioinformatics (Oxford, England) · 2024Article
- Toward an Integrated Machine Learning Model of a Proteomics Experiment.Journal of proteome research · 2023Review
- Simulation of mass spectrometry-based proteomics data with Synthedia.Bioinformatics advances · 2023Article
- SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions.PloS one · 2021Article
- Benchmarking mass spectrometry based proteomics algorithms using a simulated database.Network modeling and analysis in health informatics and bioinformatics · 2021Article
- In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics.Metabolites · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.