ArticleJournal of the American Society for Mass Spectrometry2015
From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics.
Article in Journal of the American Society for Mass Spectrometry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network.Schizophrenia (Heidelberg, Germany) · 2026Article
- Acid Cleavable Biotin-Alkyne Improves Sensitivity for Direct Detection of Biotin Labeled Peptides in Biorthogonal Noncanonical Amino Acid Tagging Analysis.Journal of proteome research · 2024Article
- Acid cleavable biotin-alkyne improves sensitivity for direct detection of biotin labeled peptides in BONCAT analysis.bioRxiv : the preprint server for biology · 2024Article
- Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2022Article
- Proteomic screen reveals diverse protein transport between connected neurons in the visual system.Cell reports · 2022Article
- Hypothetical Proteins as Predecessors of Long Non-coding RNAs.Current genomics · 2020Review
- Quantitative analysis of global protein stability rates in tissues.Scientific reports · 2020Article
- PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks.Journal of the American Society for Mass Spectrometry · 2020Article
- Structural Analysis of Hippocampal Kinase Signal Transduction.ACS chemical neuroscience · 2018Article
- Screening the Molecular Framework Underlying Local Dendritic mRNA Translation.Frontiers in molecular neuroscience · 2017Review
- Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics.Current protocols in bioinformatics · 2016Article
- Cardiovascular proteomics in the era of big data: experimental and computational advances.Clinical proteomics · 2016Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
In the last two decades, computational tools for mass spectrometry-based proteomics data analysis have evolved from a few stand-alone software solutions serving specific goals, such as the identification of amino acid sequences based on mass spectrometry spectra, to large-scale complex pipelines integrating multiple computer programs to solve a collection of problems. This software evolution has been mostly driven by the appearance of novel technologies that allowed the community to tackle complex biological problems, such as the identification of proteins that are differentially expressed in two samples under different conditions. The achievement of such objectives requires a large suite of programs to analyze the intricate mass spectrometry data. Our laboratory addresses complex proteomics questions by producing and using algorithms and software packages. Our current computational pipeline includes, among other things, tools for mass spectrometry raw data processing, peptide and protein identification and quantification, post-translational modification analysis, and protein functional enrichment analysis. In this paper, we describe a suite of software packages we have developed to process mass spectrometry-based proteomics data and we highlight some of the new features of previously published programs as well as tools currently under development. Graphical Abstract ᅟ.
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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.