RNA technologies, Год журнала: 2024, Номер unknown, С. 283 - 304
Опубликована: Янв. 1, 2024
Язык: Английский
Nature Communications, Год журнала: 2025, Номер 16(1)
Опубликована: Янв. 2, 2025
Abstract Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves accuracy depth achievable using acquisition. We introduce diaTracer, spectrum-centric computational tool optimized data. diaTracer performs three-dimensional (mass to charge ratio, retention time, mobility) peak tracing feature detection generate precursor-resolved “pseudo-tandem spectra”, facilitating direct (“spectral-library free”) identification from is stand-alone fully integrated FragPipe platform. demonstrate performance data triple-negative breast cancer, cerebrospinal fluid, plasma samples, phosphoproteomics human leukocyte antigens immunopeptidomics experiments, low-input spatial study. also show that enables unrestricted post-translational modifications open/mass-offset searches.
Язык: Английский
Процитировано
3
Nature Protocols, Год журнала: 2025, Номер unknown
Опубликована: Янв. 17, 2025
Язык: Английский
Процитировано
1
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Май 30, 2024
Abstract Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves accuracy depth achievable using DIA. We introduce diaTracer, new spectrum-centric computational tool optimized data. diaTracer performs three-dimensional (m/z, retention time, mobility) peak tracing feature detection to generate precursor-resolved “pseudo-MS/MS” spectra, facilitating direct (“spectral-library free”) identification from is stand-alone fully integrated FragPipe platform. demonstrate performance data triple-negative breast cancer (TNBC), cerebrospinal fluid (CSF), plasma samples, phosphoproteomics HLA immunopeptidomics experiments, low-input spatial study. also show that enables unrestricted post-translational modifications open/mass-offset searches.
Язык: Английский
Процитировано
3
Frontiers in Immunology, Год журнала: 2025, Номер 15
Опубликована: Янв. 6, 2025
The immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It highly dynamic and reflects the current cellular state, enabling immune system recognize abnormal conditions, such as those present in cancer cells. To precisely determine how changes processes, induced drug treatment, affect immunopeptidome, quantitative immunopeptidomics approaches are essential. meet this need, we developed a pulsed SILAC-based method for immunopeptidomics. Metabolic labeling with lysine, arginine, leucine enabled isotopic of nearly all peptides across allotypes (> 90% on average). We established data analysis workflow that integrates de novo sequencing-based tool Peptide-PRISM comprehensive peptide identification MaxQuant accurate quantification. employed strategy explore modulation upon MAPK pathway inhibition (MAPKi) investigate alterations associated early responses inhibitor treatment acquired resistance MAPKi. Our analyses demonstrated significant during MAPKi resistant state. Moreover, identified putative tumor-specific cryptic linked these processes might represent exploitable targets immunotherapy. have new mass spectrometric approach allowed us effects common inhibitors melanoma This finally led discovery potential
Язык: Английский
Процитировано
0
Molecular & Cellular Proteomics, Год журнала: 2025, Номер unknown, С. 100938 - 100938
Опубликована: Март 1, 2025
Язык: Английский
Процитировано
0
Chemical Reviews, Год журнала: 2025, Номер unknown
Опубликована: Апрель 3, 2025
The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with outside world. Many disease-associated changes are hard-wired within yet approved drugs target less than 50 proteins. In past decade, proteomics community has made significant strides in developing new technologies tailored studying surfaceome all its complexity. this review, we first dive into unique characteristics functions of emphasizing necessity specialized labeling, enrichment, proteomic approaches. An overview surfaceomics methods provided, detailing techniques measure protein expression how leads novel discovery. Next, highlight advances proximity labeling (PLP), showcasing various enzymatic photoaffinity can map protein-protein interactions membrane complexes on surface. We then review role extracellular post-translational modifications, focusing glycosylation, proteolytic remodeling, secretome. Finally, discuss identifying tumor-specific peptide MHC they have shaped therapeutic development. This emerging field neo-protein epitopes constantly evolving, where targets identified at proteome level encompass defined PTMs, complexes, dysregulated cellular tissue locations. Given functional importance biology therapy, view as a critical piece quest neo-epitope
Язык: Английский
Процитировано
0
Frontiers in Immunology, Год журнала: 2025, Номер 16
Опубликована: Апрель 24, 2025
Human leukocyte antigen (HLA) molecules are pivotal in guiding human adaptive immune responses through their presentation of peptide ligands, collectively known as the immunopeptidome. This process is central to development cancer immunotherapies, such vaccines and T-cell therapies. Profiling immunopeptidome from plasma other biofluids has gained increasing traction, it offers a minimally invasive approach for monitoring disease states toward therapy. Here we present second iteration SAPrIm, refined immunopeptidomics tool optimized soluble HLA analysis. It can up 12 samples per batch within day. In this plasma-focused iteration, identified approximately 1,200 4,000 immunopeptides 100 µL 1 mL plasma, demonstrating high reproducibility across technical replicates, biological inter-day analyses. robust highlights method's strong potential reliable relative quantification plasma-based studies. workflow positioned advance field by enabling efficient comparative analyses mid-size cohort
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июль 30, 2024
Abstract Human leukocyte antigen class I (HLA-I) molecules present short peptide sequences from endogenous or foreign proteins to cytotoxic T cells. The low abundance of HLA-I peptides poses significant technical challenges for their identification and accurate quantification. While mass spectrometry (MS) is currently a method choice direct system-wide cellular immunopeptidome, there still need enhanced sensitivity in detecting quantifying tumor specific epitopes. As gas phase separation data-dependent MS data acquisition (DDA) increased detection by up 50%, here, we aimed evaluate the performance data-independent (DIA) combination with ion mobility (diaPASEF) high-sensitivity HLA presented peptides. Our streamlined diaPASEF workflow enabled 11,412 unique 12.5 million A375 cells 3,426 8-11mers as 500,000 high reproducibility. By taking advantage binder-specific in-silico predicted spectral libraries, were able further increase number identified We applied SILAC-DIA mixture labeled peptides, calculated heavy-to-light ratios 7,742 across 5 conditions demonstrated that achieves quantitative accuracy 4-fold dilution. Finally, quantified shared neoantigens monoallelic C1R cell line model. spiking heavy synthetic verified relative abundances 13 neoantigens. Taken together, analysis workflows can peptidome coverage lower sample amounts. precision provided DIA enable quantification less abundant species such samples same background.
Язык: Английский
Процитировано
1
RNA technologies, Год журнала: 2024, Номер unknown, С. 283 - 304
Опубликована: Янв. 1, 2024
Язык: Английский
Процитировано
0