Targeted proteomics has been playing an increasingly important role in hypothesis-driven protein research and clinical bi-omarker discovery. We have previously created a workflow, Tomahto, to enable real-time targeted pathway proteomics assays using two-dimensional multiplexing technology. Coupled with the TMT 11-plex reagent, hundreds of proteins of in-terest from up to 11 samples can be targeted and accurately quantified in a single-shot experiment with remarkable sensi-tive. However, room remains to further improve sensitivity, accuracy, and throughput, especially for targeted studies de-manding a high peptide-level success rate. Here, bearing in mind the goal to improve peptide-level targeting, we introduce several new functionalities in Tomahto, featuring integration of gas-phase fractionation using the FAIMS device, an ac-companying software program (TomahtoPrimer) to customize fragmentation for each peptide target, and support for higher multiplexing capacity with the latest TMTpro18-plex reagent. We demonstrate that adding these features to the Tomahto platform significantly improves overall success rate from 89% to 98% in a single 60-min targeted assay of 290 peptides across human cell lines, while boosting quantitative accuracy via reducing TMT reporter ion interference.
[doi:10.25345/C51R6NC0G]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: TMT, targeted proteomics, intelligent data acquisition
Principal Investigators: (in alphabetical order) |
Qing Yu, University of Massachusetts Chan Medical School, USA |
Submitting User: | qingyu0126 |
Yang K, Paulo JA, Gygi SP, Yu Q.
Enhanced Sample Multiplexing-Based Targeted Proteomics with Intelligent Data Acquisition.
J Am Soc Mass Spectrom. Epub 2024 Sep 10.
Number of Files: | |
Total Size: | |
Spectra: | |
Subscribers: | |
Owner | Reanalyses | |
---|---|---|
Experimental Design | ||
Conditions:
|
||
Biological Replicates:
|
||
Technical Replicates:
|
||
Identification Results | ||
Proteins (Human, Remapped):
|
||
Proteins (Reported):
|
||
Peptides:
|
||
Variant Peptides:
|
||
PSMs:
|
||
Quantification Results | ||
Differential Proteins:
|
||
Quantified Proteins:
|
||
Browse Dataset Files | |
FTP Download Link (click to copy):
|