Advances in targeted proteomics and applications to biomedical research
Targeted proteomics technique has emerged as a powerful protein quantification tool in
systems biology, biomedical research, and increasing for clinical applications. The most …
systems biology, biomedical research, and increasing for clinical applications. The most …
Processing strategies and software solutions for data‐independent acquisition in mass spectrometry
Data‐independent acquisition (DIA) offers several advantages over data‐dependent
acquisition (DDA) schemes for characterizing complex protein digests analyzed by LC …
acquisition (DDA) schemes for characterizing complex protein digests analyzed by LC …
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
There is a need to better understand and handle the'dark matter'of proteomics—the vast
diversity of post-translational and chemical modifications that are unaccounted in a typical …
diversity of post-translational and chemical modifications that are unaccounted in a typical …
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
CC Tsou, D Avtonomov, B Larsen, M Tucholska… - Nature …, 2015 - nature.com
As a result of recent improvements in mass spectrometry (MS), there is increased interest in
data-independent acquisition (DIA) strategies in which all peptides are systematically …
data-independent acquisition (DIA) strategies in which all peptides are systematically …
Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism
A Casanovas, RR Sprenger, K Tarasov… - Chemistry & biology, 2015 - cell.com
Elucidating how and to what extent lipid metabolism is remodeled under changing
conditions is essential for understanding cellular physiology. Here, we analyzed proteome …
conditions is essential for understanding cellular physiology. Here, we analyzed proteome …
Proteomics is analytical chemistry: Fitness-for-purpose in the application of top-down and bottom-up analyses
JR Coorssen, AL Yergey - Proteomes, 2015 - mdpi.com
Molecular mechanisms underlying health and disease function at least in part based on the
flexibility and fine-tuning afforded by protein isoforms and post-translational modifications …
flexibility and fine-tuning afforded by protein isoforms and post-translational modifications …
Data-driven tool for cross-run ion selection and peak-picking in quantitative proteomics with data-independent acquisition LC–MS/MS
B Yan, M Shi, S Cai, Y Su, R Chen, C Huang… - Analytical …, 2023 - ACS Publications
Proteomics provides molecular bases of biology and disease, and liquid chromatography–
tandem mass spectrometry (LC–MS/MS) is a platform widely used for bottom-up proteomics …
tandem mass spectrometry (LC–MS/MS) is a platform widely used for bottom-up proteomics …
SuperQuant: a data processing approach to increase quantitative proteome coverage
SuperQuant is a quantitative proteomics data processing approach that uses
complementary fragment ions to identify multiple coisolated peptides in tandem mass …
complementary fragment ions to identify multiple coisolated peptides in tandem mass …
A guide to mass spectrometry-based quantitative proteomics
BJ Smith, D Martins-de-Souza… - Pre-Clinical Models …, 2019 - Springer
Proteomics has become an attractive science in the postgenomic era, given its capacity to
identify up to thousands of molecules in a single, complex sample and quantify them in an …
identify up to thousands of molecules in a single, complex sample and quantify them in an …
Peptide de novo sequencing of mixture tandem mass spectra
V Gorshkov, SYK Hotta, T Verano‐Braga… - …, 2016 - Wiley Online Library
The impact of mixture spectra deconvolution on the performance of four popular de novo
sequencing programs was tested using artificially constructed mixture spectra as well as …
sequencing programs was tested using artificially constructed mixture spectra as well as …