ReviewBiochimica et biophysica acta2014
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
Review in Biochimica et biophysica acta, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.FEMS microbiology ecology · 2016Guideline
- Open-Source and FAIR Research Software for Proteomics.Journal of proteome research · 2025Review
- Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome.Journal of clinical medicine · 2025Review
- Thermal Proteome Profiling to Identify Protein-ligand Interactions in the Apicomplexan ParasiteBio-protocol · 2021Article
- MS Amanda 2.0: Advancements in the standalone implementation.Rapid communications in mass spectrometry : RCM · 2021Article
- Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines.Proteomics · 2020Review
- Review
- Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide.Computational and structural biotechnology journal · 2018Review
- GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.PloS one · 2018Article
- Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry.Nature protocols · 2017Article
- pyQms enables universal and accurate quantification of mass spectrometry data.Molecular & cellular proteomics : MCP · 2017Article
- Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.Cell systems · 2017Article
- BioContainers: an open-source and community-driven framework for software standardization.Bioinformatics (Oxford, England) · 2017Article
- Algorithms and design strategies towards automated glycoproteomics analysis.Mass spectrometry reviews · 2017Review
- The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.Nucleic acids research · 2017Article
- Four simple recommendations to encourage best practices in research software.F1000Research · 2017Article
- Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.Bioinformatics (Oxford, England) · 2016Article
- Article
- PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.Molecular & cellular proteomics : MCP · 2016Article
- ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.Bioinformatics (Oxford, England) · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
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.