Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics

Detergent‐based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent‐bas...

Full description

Saved in:
Bibliographic Details
Published in:Proteomics (Weinheim) 2024-05, Vol.24 (10), p.e2300339-n/a
Main Authors: Nickerson, Jessica L., Gagnon, Hugo, Wentzell, Peter D., Doucette, Alan A.
Format: Article
Language:English
Subjects:
Cartridges
Chemical Precipitation
Detergents - chemistry
Digestion
Humans
Mass spectrometry
Mass spectroscopy
Peptides
Peptides - analysis
Peptides - chemistry
precipitation
Proteins
Proteome - analysis
Proteome - chemistry
Proteomes
Proteomics
Proteomics - methods
quantitation
reproducibility
Sample preparation
Sodium dodecyl sulfate
Sodium Dodecyl Sulfate - chemistry
Sodium lauryl sulfate
Variance
Workflow
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Detergent‐based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent‐based workflow for quantitative proteomics, we herein evaluate the precision of a bottom‐up sample preparation strategy incorporating cartridge‐based protein precipitation with organic solvent to deplete SDS. The variance of data‐independent acquisition (SWATH‐MS) data was isolated from sample preparation error by modelling the variance as a function of peptide signal intensity. Our SDS‐assisted cartridge workflow yield a coefficient of variance (CV) of 13%–14%. By comparison, conventional (detergent‐free) in‐solution digestion increased the CV to 50%; in‐gel digestion provided lower CVs between 14% and 20%. By filtering peptides predicting to display lower precision, we further enhance the validity of data in global comparative proteomics. These results demonstrate the detergent‐based precipitation workflow is a reliable approach for in depth, label‐free quantitative proteome analysis.
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.202300339