PXD035249

PXD035249 is an original dataset announced via ProteomeXchange.

Title	Four-dimensional proteomics analysis of human cerebrospinal fluid on a trapped ion mobility mass spectrometer using PASEF
Description	A quadrupole time-of-flight mass spectrometry coupled with a trapped ion mobility mass spectrometer operated in parallel accumulation-serial fragmentation mode has recently emerged as proteome profiling platform capable of providing four dimensional features of elution time, collision cross section, precursor and fragment ion masses of peptides. The PASEF mode has demonstrated its superior performance by providing nearly 100% ion sampling efficiency both in data-dependent acquisition and data-independent acquisition modes without sacrificing sensitivity. In addition, the substantial gain in selectivity has been proven in targeted measurements using PASEF integrated parallel reaction monitoring mode. However, because these are emerging technologies in the field of proteomics, their applicability to clinical samples has been less investigated. Cerebrospinal fluid is in direct contact with brain and has been shown to contain biomarkers related to a variety of neurological diseases although the proteomics data have been mainly generated using orbitrap-based mass spectrometers. Thus, we acquired in-depth proteome profiles of human CSF in DDA mode to generate a spectral library of 3,478 proteins. The benefit of applying the spectral library to PRM experiments was demonstrated by using CSF samples from 15 Alzheimer’s disease patients and 19 controls and utilizing the spectral library to determine elution times and ion mobility values of targeting peptide. Further, we acquired DIA data from the same CSF samples, and analyzed using the spectral library without additional efforts to generate study-specific library, which also resulted in sensitive protein identification compared to a library-free approach. Overall, we established resource of CSF proteome profiles with 4D features and demonstrated the significant gain for designing and analyzing targeted and DIA studies, which is expected to facilitate 4D proteomics of CSF to study various neurological disorders.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:48:35.946.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-11 13:32:57	ID requested
1	2023-02-28 01:43:46	announced
⏵ 2	2023-11-14 07:48:38	announced	2023-11-14: Updated project metadata.

Khomiakov IuS, Salamov RF, Semenova NA, [Age-related dynamics of the shape and size of the subpubic angle in children and adolescents]. Arkh Anat Gistol Embriol, 93(7):47-51(1987) [pubmed]

submitter keyword: 4D proteomics, and Alzheimer’s Disease, DDA-PASEF, CSF, diaPASEF, prm-PASEF

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2023/02/PXD035249

PRIDE project URI

• PRIDE
  1. PXD035249
     1. Label: PRIDE project
     2. Name: Four-dimensional proteomics analysis of human cerebrospinal fluid on a trapped ion mobility mass spectrometer using PASEF