PXD039066-1

PXD039066 is an original dataset announced via ProteomeXchange.

Title	Optimizing single cell proteomics on a trapped ion mobility spectrometry for label-free experiments
Description	Although single cell RNA-seq has had a tremendous impact on biological research, a corresponding technology for unbiased mass spectrometric analysis of single cells has only recently become available. Significant technological breakthroughs including miniaturized sample handling have enabled proteome profiling of single cells. Further, a trapped ion mobility spectrometry (TIMS) in combination with parallel accumulation-serial fragmentation operated with data-dependant acquisition mode has allowed improved proteome coverage from low-input samples. It has been demonstrated that modulating ion flux in TIMS affects overall performance of proteome profiling. However, the effect of TIMS settings for analyzing low-input samples has been less investigated. Thus, we sought to optimize conditions of TIMS in regards of ion accumulation/ramp times and ion mobility range for low-input samples. We observed that ion accumulation times of 180 ms and monitoring a narrower ion mobility range from 0.7 to 1.3 Vs cm-2 resulted in a substantial gain in the depth of proteome coverage and in detecting proteins with low abundance. We applied these optimized conditions for proteome profiling of sorted human primary T cells, which yielded an average of 365, 804, 1,116, and 1,651 proteins from single, five, ten, and forty T cells, respectively. Notably, we demonstrated that the depth of proteome coverage from low number of cells was sufficient to delineate several essential metabolic pathways and T cell receptor signaling pathway. Finally, we showed the feasibility of detecting post-translational modifications including phosphorylation and acetylation from single cells. We believe that these parameters could be applied to label-free analysis of single cells obtained from clinically relevant samples.
HostingRepository	PRIDE
AnnounceDate	2024-08-02
AnnouncementXML	Submission_2024-08-01_22:17:35.682.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	phosphorylated residue; acetylated residue
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-22 02:27:54	ID requested
⏵ 1	2024-08-01 22:17:36	announced

Mun DG, Bhat FA, Ding H, Madden BJ, Natesampillai S, Badley AD, Johnson KL, Kelly RT, Pandey A, Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst, 148(15):3466-3475(2023) [pubmed]

10.1039/d3an00080j;

submitter keyword: DDA-PASEF, primary T cells, label-free

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 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

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PRIDE project URI

• PRIDE
  1. PXD039066
     1. Label: PRIDE project
     2. Name: Optimizing single cell proteomics on a trapped ion mobility spectrometry for label-free experiments