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Published on: August 2, 2018
FAIMS-MS might contribute to phosphopeptides identification in plasma
V Besada1, Y Ramos2, L A Espinosa2
1Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology (CIGB), Havana CP: 10600, Cuba; Proteomics Laboratory, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Yangjiaqiao Street, Lengshuitan District, Yongzhou City, Hunan Province CP: 425000, China.
Optimizing the Field Asymmetric Ion Mobility Spectrometry (FAIMS) interface enhances phosphoproteome analysis. This new method increases phosphopeptide identification by 50% in complex samples like cell lines and plasma.
Area of Science:
- Proteomics
- Analytical Chemistry
- Biochemistry
Background:
- Field Asymmetric Ion Mobility Spectrometry (FAIMS) coupled with Orbitrap technology offers significant signal-to-noise enhancement.
- FAIMS improves proteome coverage by selecting ion groups and removing single-charged ions, but specific settings for phosphoproteome analysis remain underexplored.
- Previous FAIMS methods show limitations in comprehensive phosphopeptide identification.
Discussion:
- This study identifies optimal compensation voltages for tryptic phosphopeptides, revealing the importance of voltages exceeding 47 V.
- A novel experimental method using five distinct compensation voltages was developed and validated.
- The optimized FAIMS method significantly enhances phosphopeptide identification in complex biological samples.
Key Insights:
- The developed FAIMS method increases unique phosphopeptide detection by approximately 20%.
- Analysis of SH-SY5Y cell line and plasma phosphoproteomes showed a 50% increase in phosphopeptide identification compared to previous methods.
- 109 novel phosphopeptides were identified in human plasma, suggesting the release of intracellular proteins.
Outlook:
- This optimized FAIMS setup facilitates the identification of low-abundance proteins, with 60% of identified proteins being very low abundant.
- The method holds promise for advancing phosphoproteomics research, particularly in biomarker discovery and understanding cellular signaling pathways.
- Further refinement of FAIMS parameters could unlock deeper insights into complex biological systems.
