PXD040788-2

PXD040788 is an original dataset announced via ProteomeXchange.

Title	Automated sample preparation workflow for tandem mass tag-based proteomics
Description	Although tandem mass tag (TMT)-based isobaric labeling has become a powerful technique for multiplexed protein quantitation, it has not been easy to automate the workflow for widespread adoption. This is because preparation of TMT labeled peptide samples involves multiple steps ranging from protein extraction, denaturation, reduction and alkylation to tryptic digestion, desalting, labeling with TMT reagents and cleanup, all of which require a high level of proficiency. The variability resulting from multiple processing steps is inherently problematic especially with large-scale studies such as clinical studies that involve hundreds of samples where reproducibility is critical for quantitation. Here, we sought to compare the performance of a recently introduced platform, AccelerOme, for automated proteomics workflows for TMT-labeling experiments with manual processing of samples. Cell pellets were prepared and subjected to a 16-plex experiment using the automated platform and a conventional manual protocol. Single shot LC-MS/MS analysis revealed a higher number of proteins and peptides identified using the automated platform. Efficiencies of tryptic digestion, alkylation and TMT labeling were similar both in manual and automated process. In addition, comparison of quantitation accuracy and precision showed similar performance in automated workflow compared to manual sample preparation. Overall, we demonstrated that the automated platform performs at a level similar to manual process in TMT-based proteomics. We expect that the automated workflow will increasingly replace manual work and be applied to large-scale TMT-baed studies providing robust results and high sample throughput.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:09:41.532.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	TMTpro
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-11 06:24:25	ID requested
1	2023-10-24 12:21:21	announced
⏵ 2	2023-11-14 09:09:44	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:09:48	announced	2024-10-22: Updated project metadata.

Mun DG, Joshi NS, Budhraja R, Sachdeva GS, Kang T, Bhat FA, Ding H, Madden BJ, Zhong J, Pandey A, Automated Sample Preparation Workflow for Tandem Mass Tag-Based Proteomics. J Am Soc Mass Spectrom, 34(10):2087-2092(2023) [pubmed]

submitter keyword: Automation, Tandem Mass Tags, Proteomics

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

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/2023/10/PXD040788

PRIDE project URI

• PRIDE
  1. PXD040788
     1. Label: PRIDE project
     2. Name: Automated sample preparation workflow for tandem mass tag-based proteomics