@misc{10481/75779,
year = {2022},
month = {5},
url = {http://hdl.handle.net/10481/75779},
abstract = {The use of a proper sample processing methodology for maximum proteome coverage
and high-quality quantitative data is an important choice to make before initiating a liquid
chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing
workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phaseenhanced
sample preparation (SP3). We tested them on both HeLa cells and human plasma samples,
using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using
commercially available depletion mini spin columns before SP3, to increase proteome coverage in
human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the
highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use
of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins.
With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance
proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we
recommend the use of the SP3 methodology for biological sample processing, including those after
depletion of high-abundance plasma proteins.},
organization = {Research Council of Norway	295910},
publisher = {MDPI},
keywords = {Sodium dodecyl sulfate},
keywords = {Guanidinium hydrochloride},
keywords = {Liquid chromatography–mass spectrometry},
keywords = {Proteomics},
keywords = {Single-pot},
keywords = {Solid-phase-enhanced sample preparation},
keywords = {In-solution digestion},
keywords = {Plasma},
keywords = {Cells},
keywords = {Depletion},
title = {Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography–Mass Spectrometry Analysis of Human Cells and Plasma},
doi = {10.3390/molecules27113390},
author = {Neset, Lasse and Hernández Valladares, María},
}