Dataset Information

Detection and quantitation of small proteins using mass spectrometry

ABSTRACT: Small proteins or microproteins, despite long being ignored, have important roles in the regulation of larger protein complexes, metabolic pathways and gene expression. However, these proteins remain underrepresented in proteomics studies due to low detection efficiency in traditional mass spectrometry workflows. Their inherent characteristics often lead to depletion during sample preparation and a low detection efficiency in liquid chromatography-mass spectrometry (LC-MS). To improve detection and quantitation, we took advantage of the large set of documented small proteins in Escherichia coli and systematically compared and optimized different sample preparation and LC-MS approaches. We evaluated different top-down and bottom-up approaches, including data-dependent acquisition (DDA), data-independent acquisition (DIA) and parallel reaction monitoring (PRM). Our data highlight the benefit of top-down proteomics for identifying new small proteins and bottom-up preparation coupled with PRM acquisition for quantitation of protein levels in different growth conditions. Our systematic comparison can serve as a guideline for MS detection of small proteins in all organisms.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

SUBMITTER: Julian Langer

LAB HEAD: Julian D.

PROVIDER: PXD058422 | Pride | 2025-09-03

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	231123_100amolSPT_HeLa_iRT_EcUM2_FTFT_Pepsep25_75min_1_PRM.raw	Raw
	231123_100amolSPT_HeLa_iRT_EcUM2_FTFT_Pepsep25_75min_1_PRM_2.raw	Raw
	231123_100amolSPT_HeLa_iRT_EcUM2_FTFT_Pepsep25_75min_1_PRM_3.raw	Raw
	231123_10amolSPT_HeLa_iRT_EcUM2_FTFT_Pepsep25_75min_1_PRM_1.raw	Raw
	231123_10amolSPT_HeLa_iRT_EcUM2_FTFT_Pepsep25_75min_1_PRM_2.raw	Raw

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Publications

Detection and Quantitation of Small Proteins Using Mass Spectrometry.

Franco Pedro H C PHC Zeinert Rilee R Meier-Credo Jakob J Storz Gisela G Langer Julian D JD

Molecular & cellular proteomics : MCP 20250814 9

Small proteins or microproteins, despite long being ignored, have important roles in the regulation of larger protein complexes, metabolic pathways, and gene expression. However, these proteins remain under-represented in proteomics studies because of low detection efficiency in traditional mass spectrometry (MS) workflows. Their inherent characteristics often lead to depletion during sample preparation and a low detection efficiency in LC-MS. To improve detection and quantitation, we took advan ...[more]

PMID: 40818532

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