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Updated: Jul 6, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
Published on: November 17, 2019
Subcellular fractionation and proteomics of nuclear envelopes
Laurence Florens1, Nadia Korfali, Eric C Schirmer
1The Stowers Institute for Medical Research, Kansas City, MO, USA.
Abstract:
Because of its many connections to other cell systems, the nuclear envelope (NE)is essentially impossible to purify to homogeneity. To circumvent these problems, we developed a subtractive proteomics approach in which the fraction of interest and a fraction known to contaminate the fraction of interest are separately analyzed, and proteins identified in both fractions are subtracted from the data set. This requires that the contaminating fraction can be purified to homogeneity. In this case, microsomal membranes (MMs) are used to represent endoplasmic reticulum contamination, allowing the identification of transmembrane proteins specific to the NE. To circumvent problems commonly associated with analyzing membrane proteins, the multidimensional protein identification technology (MudPIT) proteomics methodology is employed.
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