PXD009342

PXD009342 is an original dataset announced via ProteomeXchange.

Title	Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster
Description	Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitations. In its simple implementation (TMT-MS2), measurements are distorted by chemical noise leading to poor measurement accuracy. The current state-of-the-art (TMT-MS3) addresses this, but requires specialized quadrupole-iontrap-Orbitrap instrumentation. The complement reporter ion approach (TMTc) produces high accuracy measurements and is compatible with many more instruments, like quadrupole-Orbitraps. However, the required deconvolution of the TMTc cluster leads to poor measurement precision. Here, we introduce TMTc+, which adds the modeling of the MS2-isolation step into the deconvolution algorithm. The resulting measurements are comparable in precision to TMT-MS3/MS2. The improved duty cycle, and lower filtering requirements make TMTc+ more sensitive than TMT-MS3 and comparable with TMT-MS2. At the same time, unlike TMT-MS2, TMTc+ is exquisitely able to distinguish signal from chemical noise even outperforming TMT-MS3. Lastly, we compare TMTc+ to quantitative label-free proteomics of total HeLa lysate and find that TMTc+ quantifies 7.8k versus 3.9k proteins in a 5-plex sample. At the same time the median coefficient of variation improves from 13% to 4%. Thus, TMTc+ advances quantitative proteomics by enabling accurate, sensitive, and precise multiplexed experiments on more commonly used instruments.
HostingRepository	PRIDE
AnnounceDate	2018-04-23
AnnouncementXML	Submission_2018-04-23_04:17:24.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Sonnett
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-27 03:55:30	ID requested
⏵ 1	2018-04-23 04:17:25	announced

Sonnett M, Yeung E, W, ü, hr M, Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster. Anal Chem, 90(8):5032-5039(2018) [pubmed]

curator keyword: Technical

submitter keyword: Quantitative Multiplexed Proteomics, TMT, MS2, MS3, TMTc, label free

Martin Wühr
contact affiliation	Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA, 08540
contact email	wuhr@princeton.edu
lab head
Matthew Sonnett
contact affiliation	Princeton University
contact email	sonnett.matt@gmail.com
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/2018/04/PXD009342

PRIDE project URI

• PRIDE
  1. PXD009342
     1. Label: PRIDE project
     2. Name: Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster