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ProteomicsExpanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS
In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase sepa...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Gallus gallus (Chicken) Equus caballus (Horse) 
2020-07-22 | PXD019926 | Pride
Faims Whole proteome Cross-linking mass spectrometry Xl-ms Orbitrap fusion lumos Cx-ms 
ProteomicsAn evaluation of high-field asymmetric-waveform ion mobility spectrometry coupled to electron-transfer/higher-energy collision dissociation for ADP-ribosylation proteomics
Objective: ADP-ribosylation is a post-translational modification that plays an important role in cellular processes. Our previous work implemented multiple gas-phase separation strategies (e.g., FAIMS) and in-source CID on the quadrupole-Orbitrap (Exploris 480) to increase the yield and acceptor sit...
ORGANISM(S): Homo sapiens (Human) 
2025-12-26 | PXD068570 | Pride
ProteomicsAn evaluation of high-field asymmetric-waveform ion mobility spectrometry coupled to electron-transfer/higher-energy collision dissociation for ADP-ribosylation proteomics
Objective: ADP-ribosylation is a post-translational modification that plays an important role in cellular processes. Our previous work implemented multiple gas-phase separation strategies (e.g., FAIMS) and in-source CID on the quadrupole-Orbitrap (Exploris 480) to increase the yield and acceptor sit...
ORGANISM(S): Homo sapiens (Human) 
2026-04-13 | PXD067389 | Pride
Macrophage Proteomics Ethcd Hcd Adp-ribosylation 
ProteomicsBoosting MS1-only proteomics with machine learning allows 2000 protein identifications in single-shot human proteome analyses using 5-minute HPLC gradients
Proteome-wide analyses rely on tandem mass spectrometry and extensive separation of proteolytic mixtures imposing considerable instrumental time consumption that is one of the main obstacles in a broader acceptance of proteomics in biomedical and clinical research. Recently, we presented a fast prot...
ORGANISM(S): Homo sapiens (Human) 
2021-03-18 | PXD023977 | Pride
Faims Fusion lumos Mass spectrometry Ms1-only Hela Protein identification 
ProteomicspFAIMS: An optimized workflow for quantitative multiplexed phosphorylation analysis using high-Field Asymmetric waveform Ion Mobility Spectrometry (FAIMS)
Protein phosphorylation is vital for the regulation of cellular signaling. Isobaric tag-based proteomic techniques, such as tandem mass tags (TMT), can measure the relative phosphorylation states of peptides in a multiplexed format. However, the overall low stoichiometry of protein phosphorylation c...
ORGANISM(S): Homo sapiens (Human) 
2020-01-10 | PXD014593 | Pride
Faims Tmt Lumos Sl-tmt Isobaric Phosphorylation 
ProteomicsGeLC-FAIMS-MS Workflow for In-Depth Middle-Down Proteomics
Middle-down proteomics is an analytical approach whereby protein samples are digested with proteases such as Glu-C to generate large peptides (>3 kDa) that are then analyzed by mass spectrometry. This method is useful for characterizing high-molecular-weight proteins that are difficult to detect by ...
ORGANISM(S): Homo sapiens (Human) 
2024-11-20 | PXD041358 | Pride
Glu-c digestion Proteoform Middle-down proteomics Lc-faims orbitrap mass spectrometry Peppi-ms Anexsp 
ProteomicsProteome analysis without chromatography: Flow injection analysis
Data demonstrating and optimizing the conditions for proteome analysis without liquid chromatography but flow injection analysis - data independent acquisition. Collected on an orbitrap fusion lumos system with FAIMS in the Coon Lab.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-03-25 | MSV000085156 | MassIVE
ProteomicsImproved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques.
Circulating antibodies provide valuable information about an individual’s immune status and constitute a significant portion of the human plasma proteome. Proteomic analysis of plasma is challenged by the large dynamic concentration range of plasma proteins, including antibodies. Peptide fractionati...
ORGANISM(S): Homo sapiens (Human) 
2024-08-09 | PXD046072 | Pride
Peptide fractionation Antibody Mass spectrometry Immune repertoire Multi-dimensional chromatography Ion-mobility Bottom-up proteomics De novo sequencing Plasma proteomics 
ProteomicsSelectivity of 2J2V for BET proteins in A549 cells
Data independent acquisition (DIA) mass spectrometry was used to study the selectivity of 2J2V for BET proteins from A549 cells. BET proteins, BRD2, BRD3 and BRD4 were observed to be degraded the most by 2J2V in comparison to MZ1 or DMSO.
ORGANISM(S): Homo sapiens (Human) 
2024-10-08 | PXD049407 | Pride
Bet proteins Dia mass spectrometry Faims-orbitrap lumos 
ProteomicsTo investigate how Trametinib affects colorectal CAFs in ECM production and remodeling
Data independent acquisition (DIA) mass spectrometry was used to study the role of the MEK1/2 inhibitor Trametinib on the ability of colorectal CAFs to produce and modify the extracellular matrix
ORGANISM(S): Homo sapiens (Human) 
2026-02-12 | PXD058691 | Pride
Cafs Trametinib Dia mass spectrometry Faims-orbitrap lumos 
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