Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice.
Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully automated multiplexed proteome profiling platform (AutoMP3) using the Hamilton Vantage liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single-shot runs, we ... More
Discovering the Radiation Biomarkers in the Plasma of Total-Body Irradiated Leukemia Patients.
AuthorsGabriela R,Vera V,Pavel R,Helena R,Igor S,Marie D,Marketa M,Alena MF,Ales T
JournalRadiation research
PubMed ID38315067
The increased risk of acute large-scale radiological exposure for the world's population underlines the need for optimal radiation biomarkers. Ionizing radiation triggers a complex response by the genome, proteome, and metabolome, all of which have been reported as suitable indicators of radiation-induced damage in vivo. This study analyzed peripheral blood samples ... More
Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags.
AuthorsZinn N,Werner T,Doce C,Mathieson T,Boecker C,Sweetman G,Fufezan C,Bantscheff M
JournalJournal of proteome research
PubMed ID33621079
Multiplexed quantitative proteomics enabled complex workflows to study the mechanisms by which small molecule drugs interact with the proteome such as thermal proteome profiling (TPP) or multiplexed proteome dynamics profiling (mPDP). TPP measures changes in protein thermal stability in response to drug treatment and thus informs on direct targets and ... More
Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses.
JournalJournal of the American Society for Mass Spectrometry
PubMed ID37163770
Proteomics research has been transformed due to high-throughput liquid chromatography (LC-MS/MS) tandem mass spectrometry instruments combined with highly sophisticated automated sample preparation and multiplexing workflows. However, scaling proteomics experiments to large sample cohorts (hundreds to thousands) requires thoughtful quality control (QC) protocols. Robust QC protocols can help with reproducibility, quantitative ... More
Proteomic Profiling of Cerebrospinal Fluid by 16-Plex TMT-Based Mass Spectrometry.
JournalMethods in molecular biology (Clifton, N.J.)
PubMed ID34905163
Mass spectrometry (MS) has become a mainstream platform for comprehensive profiling of proteome, especially with the improvement of multiplexed tandem mass tag labeling coupled with two-dimensional liquid chromatography and tandem mass spectrometry (TMT-LC/LC-MS/MS). Recently, we have established a robust method for direct profiling of undepleted cerebrospinal fluid (CSF) proteome with ... More
Integration of protein context improves protein-based COVID-19 patient stratification.
BACKGROUND: Classification of disease severity is crucial for the management of COVID-19. Several studies have shown that individual proteins can be used to classify the severity of COVID-19. Here, we aimed to investigate whether integrating four types of protein context data, namely, protein complexes, stoichiometric ratios, pathways and network degrees ... More
Professor Benedykt Dybowski, M.D. (1833-1930): physician and discoverer of the East Siberian Fauna.
AuthorsLisowski W
JournalMateria medica Polona. Polish journal of medicine and pharmacy
PubMed ID3330167
Quantitative Proteome Data Analysis of Tandem Mass Tags Labeled Samples.
AuthorsPagel O,Kollipara L,Sickmann A
JournalMethods in molecular biology (Clifton, N.J.)
PubMed ID33950506
In mass spectrometry-based proteomics, relative quantitative approaches enable differential protein abundance analysis. Isobaric labeling strategies, such as tandem mass tags (TMT), provide simultaneous quantification of several samples (e.g., up to 16 using 16plex TMTpro) owing to its multiplexing capability. This technology improves sample throughput and thereby minimizes both measurement time ... More
Labeled quantitative proteomics dataset of optogenetics induced axon regeneration in mice.
AuthorsHarvey FC,Mendoza X,Liu Y,Lee RK,Bhattacharya SK
JournalData in brief
PubMed ID35677457
This labeled quantitative proteomics dataset was collected from a transgenic channel rhodopsin mouse model (Chr2) subjected to light stimulation after traumatic optic nerve crush (ONC). Protein extraction was performed by careful mincing of the tissue in extraction buffer (TEAB, NaCl and SDS). Protein amounts were normalized across samples using dot ... More
High-Throughput and In-Depth Proteomic Profiling of 5 μL Plasma and Serum Using TMTpro 16-Plex.
AuthorsZhou Y,Sun R,Li S,Liang X,Qian L,Yue L,Guo T
JournalMethods in molecular biology (Clifton, N.J.)
PubMed ID36781780
High-throughput and in-depth proteomic analysis of plasma and serum samples remains challenging due to the presence of multiple high-abundance proteins. Here, we provide a detailed protocol for proteomic analysis of serum and plasma specimens using a high-abundance protein depletion kit and TMTpro 16-plex reagents. This method requires only 5 μL serum ... More
TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set.
The design and synthesis of a proline-based reporter isobaric Tandem Mass Tag structure (TMTpro) is presented. An analysis is made of the performance of the new TMTpro tags in comparison with the current commercially available dimethylpiperidine-reporter-based TMT10/11 reagents. The new reporter structure provides a set of 16 tags for use ... More
New Set of Isobaric Labeling Reagents for Quantitative 16Plex Proteomics.
Peptide labeling by isobaric tags is a powerful approach for the relative quantitative analysis of proteomes in multiple groups. There has been a revolution in the innovation of new isobaric reagents; however, great effort is being made to expand simultaneous labeling groups to identify more labeled peptides and reduce reporter ... More