Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry
The enormous complexity, wide dynamic range of relative protein abundance of interest (over 10 orders of magnitude), and tremendous heterogeneity (due to post-translational modifications, such as glycosylation) of the human blood plasma proteome severely challenges the capabilities of existing analytical methodologies. We describe here the comprehensive analysis of human plasma N-glycoproteins using the combination of immunoaffinity subtraction and glycoprotein capture to reduce both the protein concentration range and the overall sample complexity. Six high-abundance plasma proteins were simultaneously removed using a pre-packed, immobilized antibody column. N-linked glycoproteins were then captured from the depleted plasma using hydrazide resin, enzymatically digested, and the bound, N-linked glycopeptides were released using peptide-N-glycosidase F. Following strong cation exchange (SCX) fractionation, the deglycosylated peptides were analyzed by reversed-phase capillary liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). A total of 2140 different N-glycopeptides were confidently identified using stringent criteria, covering 371 non-redundant N-glycoproteins with the majority of them being extracellular or membrane proteins. The strategy significantly improved the detection, enabling the identification of a number of low-abundance proteins, exemplified by interleukin-1 receptor antagonist protein ({approx}200 pg/mL), cathepsin L ({approx}1 ng/mL), and transforming growth factor beta 1 ({approx}2 ng/mL). A total of 712 N-glycosylation sites were identified and the confidence of these site identifications was further validated by accurate mass measurements using high resolution liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR). This study provides the basis for future high-throughput measurements using the accurate mass and time tag approach.
- Research Organization:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 876915
- Report Number(s):
- PNNL-SA-44967; 12695; 400412000; TRN: US200608%%335
- Journal Information:
- Journal of Proteome Research, Vol. 4, Issue 6
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
ABUNDANCE
BLOOD PLASMA
CATHEPSINS
CATIONS
CHEMISTRY
CHROMATOGRAPHY
DETECTION
FRACTIONATION
GLYCOPROTEINS
GROWTH FACTORS
HYDRAZIDES
ION CYCLOTRON-RESONANCE
MASS SPECTROSCOPY
MEMBRANE PROTEINS
MODIFICATIONS
PEPTIDES
PROTEINS
RESOLUTION
Environmental Molecular Sciences Laboratory