Dataset Information

Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics

ABSTRACT: Targeted mass spectrometry (MS) approaches, which are powerful methods for uniquely and confidently quantifying a specific panel of proteins in complex biological samples, play a crucial role in validation and clinical translation of protein biomarkers discovered by global proteomic profiling. Common targeted MS methods, such as multiple reaction monitoring (MRM) and parallel-reaction monitoring (PRM), employ specific mass spectrometric technologies to quantify protein levels by comparing the transitions of specific endogenous (Endo) peptides with those of stable isotope labeled (SIL) peptide counterparts. These methods utilizing amino acid analyzed (AAA) SIL peptides warrants sensitive and precise measurements required for targeted MS assays. Compared to MRM, PRM provides higher experimental throughput by simultaneously acquiring all transitions of the target peptides and thereby compensate for different ion suppression among transitions of a target peptide. However, PRM still suffers different ion suppressions between Endo and SIL peptides due to poor spray stability as the Endo and SIL peptides were monitored at different liquid chromatography (LC) retention times. Here we introduce a new targeted MS method, termed as wideband PRM (WBPRM), designed for high-throughput targeted MS approach. WBPRM employs a wide isolation window for simultaneous fragmentations of both Endo and SIL peptides along with multiplexed single ion monitoring (SIM) scans for enhanced MS sensitivity of target peptides. Compared to PRM, WBPRM was demonstrated to provide increased sensitivity, precision, and accuracy of quantitative measurements of target peptides with increased throughput, allowing more target peptide measurements in a short experiment time. Its adaptability to a MS method provided by the manufacture makes it a facile method to implement for MS based assays, particularly in complex biological samples, where the needs for higher accuracy, sensitivity and efficiency are paramount.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Pancreas, Hela Cell

SUBMITTER: Dowoon Nam

LAB HEAD: Sang-Won Lee

PROVIDER: PXD048271 | Pride | 2024-08-14

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Cys_5Pepmix_20fmol_DDA_target_check_120min_1_C1_100923.raw	Raw
	Cys_5Pepmix_20fmol_PDAC132_7ug_PRM_120min_1_C1_101023.raw	Raw
	Cys_5Pepmix_20fmol_PDAC132_7ug_SIM_WBPRM_120min_C1_053123.raw	Raw
	Cys_5Pepmix_20fmol_PDAC132_7ug_SIM_WBPRM_120min_C1_053123_Results_10.0ppm.txt	Txt
	PRM_HeLa_0_1ug_Pepmix_1_120min_C2_040723.raw	Raw

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Publications

Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics.

Nam Dowoon D Ji Minyoung M Kang Chaewon C Kim Hokeun H Yang Hyunju H Bok Kwon Hee KH Bae Jingi J Hong Jiwon J Lee Sang-Won SW

Analytical chemistry 20240612 25

Targeted mass spectrometry (MS) approaches, which are powerful methods for uniquely and confidently quantifying a specific panel of proteins in complex biological samples, play a crucial role in validating and clinically translating protein biomarkers discovered through global proteomic profiling. Common targeted MS methods, such as multiple reaction monitoring (MRM) and parallel-reaction monitoring (PRM), employ specific mass spectrometric technologies to quantify protein levels by comparing th ...[more]

PMID: 38864836

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