SynthesisJournal of the American Society for Mass Spectrometry2015
Limitations of Mass Spectrometry-Based Peptidomic Approaches.
Synthesis in Journal of the American Society for Mass Spectrometry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- High-resolution nanopore peptide sensing, profiling and sequence assembly.Nature nanotechnology · 2026Article
- Peptides from General By-Products: Unveiling Their Potential Biological Activities in Human Health.Molecules (Basel, Switzerland) · 2025Review
- Proteomics and bioinformatics guided discovery of microalgal multifunctional peptides for novel nutraceutical applications.Bioprocess and biosystems engineering · 2025Article
- Organic Fusion of Molecular Simulation and Wet-Lab Validation: A Promising High-Throughput Strategy for Screening Bioactive Food Peptides.Foods (Basel, Switzerland) · 2025Review
- Positional distribution and conservation of major phosphorylated sites in the human kinome.Frontiers in molecular biosciences · 2025Article
- Peptidomic analysis of endogenous and bacterial protease activity in human plasma and wound fluids.iScience · 2024Article
- Quantitative Peptidomics Using Reductive Methylation of Amines.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Quantitative Peptidomics: General Considerations.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Integrating a Multi-label Deep Learning Approach with Protein Information to Compare Bioactive Peptides in Brain and Plasma.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Origins, Technological Advancement, and Applications of Peptidomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Deciphering Proteomic Expression in Inflammatory Disorders: A Mass Spectrometry Exploration Comparing Infectious, Noninfectious, and Traumatic Brain Injuries in Human Cerebrospinal Fluid.Neurotrauma reports · 2024Article
- Uncovering Novel Roles of miR-122 in the Pathophysiology of the Liver: Potential Interaction with NRF1 and E2F4 Signaling.Cancers · 2023Article
- DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins.Methods in enzymology · 2023Article
- Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing.ACS nano · 2022Article
- Na,K-ATPase α1 and β-subunits show distinct localizations in the nervous tissue of the large milkweed bug.Cell and tissue research · 2022Article
- Investigating the Short Peptidome Profile of Italian Dry-Cured Ham at Different Processing Times by High-Resolution Mass Spectrometry and Chemometrics.International journal of molecular sciences · 2022Article
- Two Metabolic Fuels, Glucose and Lactate, Differentially Modulate Exocytotic Glutamate Release from Cultured Astrocytes.Neurochemical research · 2021Article
- Emerging functions of branched ubiquitin chains.Cell discovery · 2021Review
- MultiPep: a hierarchical deep learning approach for multi-label classification of peptide bioactivities.Biology methods & protocols · 2021Article
- Substrate Specificity and Structural Modeling of Human Carboxypeptidase Z: A Unique Protease with a Frizzled-Like Domain.International journal of molecular sciences · 2020Article
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Abstract
Mass spectrometry-based peptidomic approaches are powerful techniques to detect and identify the peptide content of biological samples. The present study investigated the limitations of peptidomic approaches using trimethylammonium butyrate isotopic tags to quantify relative peptide levels and Mascot searches to identify peptides. Data were combined from previous studies on human cell lines or mouse tissues. The combined databases contain 2155 unique peptides ranging in mass from 444 to 8765 Da, with the vast majority between 1 and 3 kDa. The amino acid composition of the identified peptides generally reflected the frequency in the Eukaryotic proteome with the exception of Cys, which was not present in any of the identified peptides in the free-SH form but was detected at low frequency as a disulfide with Cys residues, a disulfide with glutathione, or as S-cyanocysteine. To test if the low detection rate of peptides smaller than 500 Da, larger than 3 kDa, or containing Cys was a limitation of the peptidomics procedure, tryptic peptides of known proteins were processed for peptidomics using the same approach used for human cell lines and mouse tissues. The identified tryptic peptides ranged from 516 to 2418 Da, whereas the theoretical digest ranged from 217 to 7559 Da. Peptides with Cys were rarely detected and, if present, the Cys was usually modified S-cyanocysteine. Additionally, peptides with mono- and di-iodo Tyr and His were identified. Taken together, there are limitations of peptidomic techniques, and awareness of these limitations is important to properly use and interpret results. Graphical Abstract ᅟ.
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