Protein identification pipeline for the homology-driven proteomics
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Updated: Jul 3, 2026

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
Published on: November 13, 2021
Magno Junqueira1, Victor Spirin, Tiago Santana Balbuena
1Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
Abstract:
Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ Orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download.
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