Featured
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Article
| Open Access
Systematic discovery of neoepitope–HLA pairs for neoantigens shared among patients and tumor types
A large resource of shared tumor neoepitopes aims to accelerate cancer immunotherapy.
- Hem R. Gurung
- , Amy J. Heidersbach
- & Christopher M. Rose
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Brief Communication
| Open Access
Spatial multimodal analysis of transcriptomes and metabolomes in tissues
Metabolites and RNA in a tissue section are profiled simultaneously.
- Marco Vicari
- , Reza Mirzazadeh
- & Joakim Lundeberg
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Article |
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors
A computational pipeline identifies tumor antigen post-translational modifications guiding immune responses.
- Assaf Kacen
- , Aaron Javitt
- & Yifat Merbl
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Research Briefing |
Framework for multiplicative scaling of single-cell proteomics
Many biomedical questions demand scalable, deep, and accurate proteome analysis of small samples, including single cells. A scalable framework of multiplexed data-independent acquisition for mass spectrometry enables time saving by parallel analysis of both peptide ions and protein samples, thereby realizing multiplicative gains in throughput.
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Article |
Increasing the throughput of sensitive proteomics by plexDIA
Proteomics of small sample sizes using data-independent acquisition methods achieves higher throughput with multiplexing.
- Jason Derks
- , Andrew Leduc
- & Nikolai Slavov
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Brief Communication |
Enhancing untargeted metabolomics using metadata-based source annotation
Metabolomics is improved by using a reference library of both known and unknown molecules.
- Julia M. Gauglitz
- , Kiana A. West
- & Pieter C. Dorrestein
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Brief Communication |
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
A machine learning workflow enables auto-deconvolution of gas chromatography–mass spectrometry data.
- Alexander A. Aksenov
- , Ivan Laponogov
- & Kirill Veselkov
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Letter |
Detection of SARS-CoV-2 in nasal swabs using MALDI-MS
SARS-CoV-2 is reliably detected in nasal swab samples using mass spectrometry and machine learning analysis.
- Fabiane M. Nachtigall
- , Alfredo Pereira
- & Leonardo S. Santos
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Brief Communication |
A lipidome atlas in MS-DIAL 4
Mass spectral fragmentations of lipids across 117 lipid subclasses are presented in a lipidome atlas.
- Hiroshi Tsugawa
- , Kazutaka Ikeda
- & Makoto Arita
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Resource |
Global landscape of cell envelope protein complexes in Escherichia coli
A survey of cell envelope proteins and their interacting partners in E. coli by mass spectrometry reveals insights into essential bacterial processes.
- Mohan Babu
- , Cedoljub Bundalovic-Torma
- & Andrew Emili
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Analysis |
A multicenter study benchmarks software tools for label-free proteome quantification
LFQbench, a software tool to assess the quality of label-free quantitative proteomics analyses, enables developers to benchmark and improve analytic methods.
- Pedro Navarro
- , Jörg Kuharev
- & Stefan Tenzer
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Resource |
Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling
Proteomics, lipidomics and metabolomics of single gene deletion yeast strains sheds light on mitochondrial protein biology.
- Jonathan A Stefely
- , Nicholas W Kwiecien
- & Joshua J Coon
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Perspective |
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
GNPS is an open-access community-curated analysis platform for sharing natural product mass spectrometry data that enables continuous, automatic reanalysis of deposited 'living' data sets.
- Mingxun Wang
- , Jeremy J Carver
- & Nuno Bandeira
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News Feature |
Technology comes to typing
As mass spectrometry makes inroads into pathogen identification in the clinical laboratory, deep sequencing—even nanopore sequencing—is waiting in the wings. Jeffrey L. Fox investigates.
- Jeffrey L Fox
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Correspondence |
Metabolomic data streaming for biology-dependent data acquisition
- Duane Rinehart
- , Caroline H Johnson
- & Gary Siuzdak
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Correspondence |
A cross-platform toolkit for mass spectrometry and proteomics
- Matthew C Chambers
- , Brendan Maclean
- & Parag Mallick
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News & Views |
Streamlining biomarker discovery
Integrating targeted mass spectrometry into proteomic pipelines speeds the validation of disease biomarkers.
- Martin Latterich
- & Jan E Schnitzer
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Correspondence |
ProHits: integrated software for mass spectrometry–based interaction proteomics
- Guomin Liu
- , Jianping Zhang
- & Anne-Claude Gingras
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Perspective |
Options and considerations when selecting a quantitative proteomics strategy
- Bruno Domon
- & Ruedi Aebersold
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News & Views |
Enriching quantitative proteomics with SIN
A new metric called the normalized spectral index (SIN) provides a simple way to quantify and compare label-free proteomics data.
- Mihaela E Sardiu
- & Michael P Washburn
Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition