ArticleNature communications2024
AlphaPept: a modern and open framework for MS-based proteomics.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed, 53 citations in OpenAlex.
- The diverse functions of viral microproteins.bioRxiv : the preprint server for biology · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Self-assembling proteins compose the chemically resistant shell biomaterial of planktonic tintinnid ciliates.Nature communications · 2026Article
- DDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics.Nature communications · 2026Article
- From Neoantigens to Nanocarriers: Modern Methods and Modalities in Using Peptides for Cancer Vaccination.Biochemistry · 2026Review
- Sensitive detection of cancer antigens enabled by user-defined peptide libraries.Nature biotechnology · 2026Article
- Vibe Coding Omics Data Analysis Applications.Journal of proteome research · 2026Article
- QproMS: a web application for label-free proteomic data analysis.Bioinformatics advances · 2026Article
- Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.Nature communications · 2025Article
- Nova: A Library for Rapid Development of Mass Spectrometry Software Applications.Journal of the American Society for Mass Spectrometry · 2025Article
- A substrate-multiplexed platform for profiling enzymatic potential of plant family 1 glycosyltransferases.Nature communications · 2025Article
- Tandem Mass Tags Quantitative Proteomics Reveal the Mechanism by Which Paeoniflorin Regulates the PI3K/AKT and BDNF/CREB Signaling Pathways to Inhibit Parkinson's Disease.International journal of molecular sciences · 2025Article
- Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment.Nature methods · 2025Article
- Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.Journal of proteome research · 2025Article
- Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics.Analytical chemistry · 2025Review
- The hidden bacterial microproteome.Molecular cell · 2025Article
- Review
- Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species.Computational and structural biotechnology journal · 2025Article
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
- Bridging the Gap From Proteomics Technology to Clinical Application: Highlights From the 68th Benzon Foundation Symposium.Molecular & cellular proteomics : MCP · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
Abstract
In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making efficient analysis a principal challenge. A plethora of different computational tools can process the MS data to derive peptide and protein identification and quantification. However, during the last years there has been dramatic progress in computer science, including collaboration tools that have transformed research and industry. To leverage these advances, we develop AlphaPept, a Python-based open-source framework for efficient processing of large high-resolution MS data sets. Numba for just-in-time compilation on CPU and GPU achieves hundred-fold speed improvements. AlphaPept uses the Python scientific stack of highly optimized packages, reducing the code base to domain-specific tasks while accessing the latest advances. We provide an easy on-ramp for community contributions through the concept of literate programming, implemented in Jupyter Notebooks. Large datasets can rapidly be processed as shown by the analysis of hundreds of proteomes in minutes per file, many-fold faster than acquisition. AlphaPept can be used to build automated processing pipelines with web-serving functionality and compatibility with downstream analysis tools. It provides easy access via one-click installation, a modular Python library for advanced users, and via an open GitHub repository for developers.
Indexed as
Identifiers
What OpenQuestion holds
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.