ArticleMolecular & cellular proteomics : MCP2021
AlphaTims: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization.
Article in Molecular & cellular proteomics : MCP, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- TIMSImaging: an open and interoperable workflow for trapped ion mobility mass spectrometry imaging data processing and visualization.Bioinformatics (Oxford, England) · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Full-DIA enables complete single-cell proteomics from diaPASEF using deep learning.Genome biology · 2026Article
- ProteoGyver: a fast, user-friendly tool for routine QC and analysis of MS-based proteomics data.Bioinformatics (Oxford, England) · 2026Article
- Trapped Ion Mobility Improves Annotation Accuracy in LC-HRMS Screening Applications for Exposomics.Analytical chemistry · 2025Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.Journal of proteome research · 2025Article
- SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run.Journal of proteome research · 2025Article
- Multimodal single cell-resolved spatial proteomics reveal pancreatic tumor heterogeneity.Nature communications · 2024Article
- M2ara: unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays.Bioinformatics (Oxford, England) · 2024Article
- The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics?Journal of proteome research · 2024Review
- Computational tools and algorithms for ion mobility spectrometry-mass spectrometry.Proteomics · 2024Review
- DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool.Journal of chemical information and modeling · 2024Article
- Uncovering Distinct Peptide Charging Behaviors in Electrospray Ionization Mass Spectrometry Using a Large-Scale Dataset.Journal of the American Society for Mass Spectrometry · 2024Article
- Nanospray Desorption Electrospray Ionization (Nano-DESI) Mass Spectrometry Imaging with High Ion Mobility Resolution.Journal of the American Society for Mass Spectrometry · 2023Article
- A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry.bioRxiv : the preprint server for biology · 2023Article
- Emerging Computational Methods in Mass Spectrometry Imaging.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Review
- Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF.Molecular & cellular proteomics : MCP · 2022Article
- TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-resolution MS-based proteomics generates large amounts of data, even in the standard LC-tandem MS configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich datasets. Taking trapped ion mobility spectrometry (TIMS) on a quadrupole TOF (Q-TOF) platform as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of minutes (LC), milliseconds (TIMS), and microseconds (TOF). In our open-source AlphaTims package, data are indexed, accessed, and visualized by a combination of tools of the scientific Python ecosystem. We interpret unprocessed data as a sparse four-dimensional matrix and use just-in-time compilation to machine code with Numba, accelerating our computational procedures by several orders of magnitude while keeping to familiar indexing and slicing notations. For samples with more than six billion detector events, a modern laptop can load and index raw data in about a minute. Loading is even faster when AlphaTims has already saved indexed data in an HDF5 file, a portable scientific standard used in extremely large-scale data acquisition. Subsequently, data accession along any dimension and interactive visualization happens in milliseconds. We have found AlphaTims to be a key enabling tool to explore high-dimensional LC-TIMS-Q-TOF data and have made it freely available as an open-source Python package with a stand-alone graphical user interface at https://github.com/MannLabs/alphatims or as part of the AlphaPept 'ecosystem'.
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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.