PXD068463
PXD068463 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | High Dynamic Range peptide mass spectrometry using segmented precursor ions accumulation - Plasma |
| Description | Limited sensitivity and depth of proteome sampling in experiments using Data-Dependent Acquisition (DDA) mass spectrometry are usually attributed to insufficient rate of fragmentation spectra acquisition relative to the number of co-eluting potential targets. Here we demonstrated that limited sensitivity and dynamic range of MS1 scans reduces the detection of low intensity ion, and thus their selection for fragmentation. As abundant ions occupy a large fraction of the ion accumulation capacity, we sought to improve MS1 detection of rare analytes by an easily implementable strategy based on gas-phase segmentation of the MS1 scan range, followed by co-accumulation and detection of all ions. The quadrupolar isolation windows used to segment the MS1 scan range are designed to transmit on average an equal number of charges, consistent with the parameter used by many recent mass spectrometers to regulate ion trap filling. This strategy, which we named High Dynamic Range MS1 (HDR-MS1), reduces the contribution of abundant ions to reaching the maximum ion capacity. As a result, HDR MS1 showed improved dynamic range and sensitivity compared to conventional full range scans, resulting in higher number of peptides and protein identifications under identical MS2 parameters, less redundant precursor ion sampling, and higher rate of quantified precursor ions. HDR MS1 scans are compatible with any DDA precursor selection filter and MS2 parameter, and the generated files can be analyzed using any software for peptide-spectral matching and quantification. This experiments refer to the plasma analysis |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-10-14 |
| AnnouncementXML | Submission_2025-10-14_07:22:26.454.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Paolo Cifani |
| SpeciesList | scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090; |
| ModificationList | Oxidation; Carboxymethyl |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-09-17 13:16:39 | ID requested | |
| ⏵ 1 | 2025-10-14 07:22:27 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: gas-phase fractionation, DDA, Mouse plasma, DatasetType:Proteomics |
Contact List
| Paolo Cifani | |
|---|---|
| contact affiliation | Cold Spring Harbor Laboratory |
| contact email | cshl.mass.spec@gmail.com |
| lab head | |
| Paolo Cifani | |
| contact affiliation | Cold Spring Harbor Laboratory |
| contact email | cshl.mass.spec@gmail.com |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v10/MSV000099211/ |
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