ArticleJournal of proteome research2014
Accurate label-free protein quantitation with high- and low-resolution mass spectrometers.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
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- When less is more: Counterintuitive stoichiometries and cellular abundances are essential for ABC transporters' function.Science advances · 2025Article
- Non-invasive molecular species identification using spider silk proteomics.Scientific reports · 2025Article
- Measurement of absolute abundance of crystallins in human and αA N101D transgenic mouse lenses usingExperimental eye research · 2024Article
- Quantification of Histone H1 Subtypes Using Targeted Proteomics.Biomolecules · 2024Article
- Proteomes of plasmodium knowlesi early and late ring-stage parasites and infected host erythrocytes.Journal of proteomics · 2024Article
- From the outer space to the inner cell: deconvoluting the complexity ofMicrobiology spectrum · 2024Article
- Differential Expression of Proteins Associated with Bipolar Disorder as Identified Using the PeptideShaker Software.International journal of molecular sciences · 2023Article
- Deciphering intercellular signaling complexes by interaction-guided chemical proteomics.Nature communications · 2023Article
- GIPC3 couples to MYO6 and PDZ domain proteins, and shapes the hair cell apical region.Journal of cell science · 2023Article
32 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
Label-free quantitation of proteins analyzed by tandem mass spectrometry uses either integrated peak intensity from the parent-ion mass analysis (MS1) or features from fragment-ion analysis (MS2), such as spectral counts or summed fragment-ion intensity. We directly compared MS1 and MS2 quantitation by analyzing human protein standards diluted into Escherichia coli extracts on an Orbitrap mass spectrometer. We found that summed MS2 intensities were nearly as accurate as integrated MS1 intensities, and both outperformed MS2 spectral counting in accuracy and linearity. We compared these results to those obtained from two low-resolution ion-trap mass spectrometers; summed MS2 intensities from LTQ and LTQ Velos instruments were similar in accuracy to those from the Orbitrap. Data from all three instruments are available via ProteomeXchange with identifier PXD000602. Abundance measurements using MS1 or MS2 intensities had limitations, however. While measured protein concentration was on average well-correlated with the known concentration, there was considerable protein-to-protein variation. Moreover, not all human proteins diluted to a mole fraction of 10(-3) or lower were detected, with a strong falloff below 10(-4) mole fraction. These results show that MS1 and MS2 intensities are simple measures of protein abundance that are on average accurate but should be limited to quantitation of proteins of intermediate to higher fractional abundance.
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