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The LC-MSMS technique identifies the difference in modification levels between two proteins

ABSTRACT: Mass spectrometry has been used as a useful tool to determine the degree of protein modification. In this study, the degree of phosphorylation between two materials, TaHAKAIR and TaHAKAIS, was identified by technique. There is a key amino acid variation in TaHAKAIR and TaHAKAIS. The phosphorylation level of TaHAKAIR and TaHAKAIS at this amino acid site was significantly changed by mass spectrometry, and the phosphorylation level of TaHAKAIR was the highest.

INSTRUMENT(S): ultraflex

ORGANISM(S): Triticum Aestivum (wheat)

TISSUE(S): Leaf

SUBMITTER: 俊郭

LAB HEAD: Jun Guo

PROVIDER: PXD062647 | Pride | 2025-04-06

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20250402_Yang_TaHAKAIR_1_30min_DDA_Slot1-20_1_4191.d.zip	Other
	20250402_Yang_TaHAKAIR_2_30min_DDA_Slot1-20_1_4191.d.zip	Other
	20250402_Yang_TaHAKAIR_3_30min_DDA_Slot1-20_1_4191.d.zip	Other
	20250402_Yang_TaHAKAIS_1_30min_DDA_Slot1-20_1_4191.d.zip	Other
	20250402_Yang_TaHAKAIS_2_30min_DDA_Slot1-20_1_4191.d.zip	Other

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Project description:The pathological hallmark of amyotrophic lateral sclerosis (ALS) is the presence of cytoplasmic inclusions, containing C-terminal fragments of the protein TDP-43. Here, we tested the hypothesis that highly sensitive mass spectrometry with parallel reaction monitoring (MS-PRM) can generate a high-resolution map of pathological TDP-43 peptide ratios to form the basis for quantitation of abnormal C-terminal TDP-43 fragment enrichment. Human cortex and spinal cord, microscopically staged for the presence of phosphoTDP-43, p-tau, alpha-synuclein and beta-amyloid pathology, were biochemically fractionated and analysed by immunoblot and MS for detection of full-length and truncated (disease-specific) TDP-43 peptides. This informed synthesis of heavy isotope-labelled peptides for the absolute quantification of TDP-43 by MS-PRM across 16 ALS, 8 Parkinson’s and 8 Alzheimer’s disease and 8 aged control cases. We confirmed by immunoblot the previously described enrichment of pathological C-terminal fragments in ALS-TDP urea fractions. Subsequent MS analysis resolved specific TDP-43 N- and C-terminal peptides, including a novel N-terminal truncation site-specific peptide. Absolute quantification of peptides by MS-PRM showed an increased C:N-terminal TDP-43 peptide ratio in ALS-TDP brain compared to normal and disease controls. A C:N-terminal ratio >1.5 discriminated ALS from controls with a sensitivity of 100% (CI 79.6-100) and specificity of 100% (CI 68-100), and from Parkinson’s and Alzheimer’s disease with a sensitivity of 93% (CI 70-100) and specificity of 100% (CI 68-100). N-terminal Truncation site-specific peptides were increased in ALS in line with C-terminal fragment enrichment, but also found in a proportion of Alzheimer cases with normal C:N-terminal ratio but coexistent TDP-43 pathology. In conclusion this is a novel, sensitive and specific method to quantify the enrichment of pathological TDP-43 fragments in human brain, which could form the basis for an antibody-free assay. Our methodology has the potential to help clarify if specific pathological TDP-43 peptide signatures are associated with primary or secondary TDP-43 proteinopathies.

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The LC-MSMS technique identifies the difference in modification levels between two proteins

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