ArticleAnalytical chemistry2018
Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics.
Article in Analytical chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 76 citations in OpenAlex.
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- Benchmarking In-Cell Proteomics for Profiling Neuroblastoma Cell Differentiation and the Ubiquitin-Proteasome System.Journal of proteome research · 2025Article
- The Importance of Denaturing Conditions for Protein and Peptide Quantification by Tryptophan Fluorescence.ACS omega · 2025Article
- Proteome-Based Maternal Plasma and Serum Biomarkers for Preeclampsia: A Systematic Review and Meta-Analysis.Life (Basel, Switzerland) · 2025Review
- Simple In-Cell Processing Enables Deep Proteome Analysis of Low-InputAnalytical chemistry · 2025Article
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- Standardizing Protein Corona Characterization in Nanomedicine: A Multicenter Study to Enhance Reproducibility and Data Homogeneity.Nano letters · 2024Article
- Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics.mSystems · 2024Article
- Memory effects of prior subculture may impact the quality of multiomic perturbation profiles.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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- Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches.Journal of extracellular vesicles · 2024Article
- Proteome encoded determinants of protein sorting into extracellular vesicles.Journal of extracellular biology · 2024Article
- Comparison of in-gel and in-solution proteolysis in the proteome profiling of organ perfusion solutions.Clinical proteomics · 2023Article
- Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma.International journal of molecular sciences · 2023Article
- High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation.Nature protocols · 2023Review
- ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues.Analytical chemistry · 2023Article
- Comparative analysis of proteomes and transcriptomes revealed the molecular mechanism of development and nutrition ofFrontiers in nutrition · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-filter (OFD), and on-pellet digestion (OPD) workflows on the basis of targeted (QconCAT-multiple reaction monitoring (MRM) method for mitochondrial proteins) and discovery proteomics (data-dependent acquisition, DDA) analyses using three different human head and neck tissues (i.e., nasal polyps, parotid gland, and palatine tonsils). Our study reveals differences between the sample preparation methods, for example, with respect to protein and peptide losses, quantification variability, protocol-induced methionine oxidation, and asparagine/glutamine deamidation as well as identification of cysteine-containing peptides. However, none of the methods performed best for all types of tissues, which argues against the existence of a universal sample preparation method for proteome analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.