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UnknownPrior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments.
Not available
S-EPMC9204819 | biostudies-literature
ProteomicsMethodologies comparison of porcine lung tissue
Mechanistic study of H2S interference on swine, we used TMT-based comparative proteomics of lung tissues from control and hydrogen sulfide (H2S) breathing swines as a test case for evaluation of MS2, SPS MS3 and RTS-MS3 acquisition methods in both Orbitrap Fusion and Orbitrap Eclipse.
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2023-06-02 | PXD020392 | Pride
Synchronous precursor selection Mass spectrometry Isobaric tandem mass tags Real-time search Quantitative proteomics Lung tissues 
ProteomicsThe GF-NEO Discovery Platform: A Systems-Level Approach to Analyzing and Validating Fusion Neoantigens in Pediatric Cancer
Gene fusions (GFs) are critical events in pediatric oncology, often serving as oncogenic drivers. However, fusion proteins and their derived neoantigens (GF-NEOs) remain underexplored for targeted immunotherapy. We developed ProteoFusioNEO, a computational tool for in silico translation of transcrip...
ORGANISM(S): Homo sapiens (Human) 
2025-11-26 | PXD063253 | Pride
ProteomicsSupporting raw MS data for paper (doi:10.1038/s41589-025-01894-4) by Raiff A., Zhao Z. et al (2025), titled "TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6"
Supporting raw MS data for paper (doi:10.1038/s41589-025-01894-4) by Raiff A., Zhao Z. et al (2025), titled "TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6". Index of MS files and labels Supplementary Table 1 - HEK293T - Proteome (CZ-1-23 | Unimod:35; 737; 4 | 126 -...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-08-23 | MSV000095689 | MassIVE
ProteomicsMonitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top-down and middle-down mass spectrometry
We propose here a workflow based on an automated immunocapture followed by top-down and middle-down LC-MS/MS approaches to characterize mAb proteoforms spiked in mouse plasma. We demonstrate the applicability of our workflow on a large concentration range using pembrolizumab as a model. We also comp...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2024-08-27 | PXD040896 | Pride
Immunocapture Monoclonal antibody Proteoforms Middle-down mass spectrometry Top-down mass spectrometry 
UnknownImproved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry.
Not available
S-EPMC7550239 | biostudies-literature
ProteomicsTop-down proteome of de-fatted Bos taurus milk from an animal with clinical mastitis
Quarter-milk samples were collected from a cow with clinical mastitis on day 13 and day 16 postpartum. Milk was collected from a clinical quarter with signs of abnormality (i.e., flakes, clots, blood) and one normal quarter of the same animal. Milk samples were processed with the MPLEx protocol (ht...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) 
2022-02-09 | MSV000088805 | MassIVE
UnknownDevelopment of novel methods for non-canonical myeloma protein analysis with an innovative adaptation of immunofixation electrophoresis, native top-down mass spectrometry, and middle-down de novo sequencing.
Not available
S-EPMC8055720 | biostudies-literature
ProteomicsCrosslinking/mass spectrometry analysis of Human Separase-Scc1-fusion and cohesin SMC1/SMC3 complexes
In this study, we employed the photoactivatable crosslinker (sulfo-SDA) to investigate protein-protein interaction between human Separase-Scc1 fusion protein and SMC1/SMC3 cohesin subunits complex in the presence of DNA.
ORGANISM(S): Homo sapiens (Human) 
2025-08-28 | PXD061667 | Pride
Sulfo-sda Smc1 Smc3 Scc1 Separase Xlms 
ProteomicsMiProChip A microfluidic device for high-throughput single-cell proteomics via multiplexed isobaric labeling
which is character 311: The MiProChip project presents a microfluidic platform for high-throughput single-cell proteomics, integrating on-chip lysis, digestion, and TMT-based labeling to achieve efficient and low-contamination proteome processing. This dataset includes (1) manually processed single-...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2025-11-05 | MSV000099763 | MassIVE
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