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Generalizable direct protein sequencing with InstaNexus

ABSTRACT: Critical protein therapeutics, such as antibodies and nanobodies, are often not encoded in reference genomes, limiting their accurate characterization via standard proteomics. Current methods rely on indirect inference, fragmented outputs, and labor-intensive workflows, which hinder functional insights and routine application. Here, we present a generalizable, end-to-end workflow for direct protein sequencing, combining streamlined sample preparation, AI-driven de novo peptide sequencing, and tailored assembly to reconstruct contiguous protein sequences. A novel composite scoring framework prioritizes longer assemblies and coverage, enhancing accuracy and reducing ambiguity. Validation across diverse protein modalities demonstrates its utility and ability to robustly reconstruct functionally critical regions essential for optimizing therapeutic efficacy, stability, and immunogenicity. This workflow advances precision proteomics with promising applications in therapeutic discovery, immune profiling, and protein engineering.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Bos Taurus (bovine)

SUBMITTER: Konstantinos Kalogeropoulos

LAB HEAD: Konstantinos Kalogeropoulos

PROVIDER: PXD066160 | Pride | 2026-02-23

REPOSITORIES: Pride

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			Action	DRS
	20240315_KMJ_Kwando_MVL_Easy15_35min_1835_DDA_50ng_ProtK_1.raw	Raw
	20240315_KMJ_Kwando_MVL_Easy15_35min_1835_DDA_50ng_ProtK_2.raw	Raw
	20240315_KMJ_Kwando_MVL_Easy15_35min_1835_DDA_50ng_ProtK_3.raw	Raw
	20240315_KMJ_Kwando_MVL_Easy15_35min_1835_DDA_50ng_ProtK_4.raw	Raw
	20240315_KMJ_Kwando_MVL_Easy15_35min_1835_DDA_50ng_ProtK_5.raw	Raw

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