ArticleJournal of proteome research2011
A novel alignment method and multiple filters for exclusion of unqualified peptides to enhance label-free quantification using peptide intensity in LC-MS/MS.
Article in Journal of proteome research, 2011. 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.
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- Exogenous Gene Transmission of Isocitrate Dehydrogenase 2 Mimics Ischemic Preconditioning Protection.Journal of the American Society of Nephrology : JASN · 2018Article
- Cholesterol trafficking and raft-like membrane domain composition mediate scavenger receptor class B type 1-dependent lipid sensing in intestinal epithelial cells.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2018Article
- On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2018Article
- Delineation of Molecular Pathways Involved in Cardiomyopathies Caused by Troponin T Mutations.Molecular & cellular proteomics : MCP · 2016Article
- Label-free proteomic methodology for the analysis of human kidney stone matrix composition.Proteome science · 2016Article
- Cancer and Chemotherapy Contribute to Muscle Loss by Activating Common Signaling Pathways.Frontiers in physiology · 2016Article
- Excess TGF-β mediates muscle weakness associated with bone metastases in mice.Nature medicine · 2015Article
- Proteomic Profiling of Hematopoietic Stem/Progenitor Cells after a Whole Body Exposure of CBA/CaJ Mice to Titanium (Proteomes · 2015Article
- Proteomic profiling of human sera for discovery of potential biomarkers to monitor abstinence from alcohol abuse.Electrophoresis · 2015Article
- Distinctive and pervasive alterations in aqueous humor protein composition following different types of glaucoma surgery.Molecular vision · 2015Article
- Bayesian proteoform modeling improves protein quantification of global proteomic measurements.Molecular & cellular proteomics : MCP · 2014Article
- Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression patterns.Nanotoxicology · 2014Article
- Quantitative proteomics in cardiovascular research: global and targeted strategies.Proteomics. Clinical applications · 2014Review
- Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.Journal of proteome research · 2014Article
- Loss of FHL1 induces an age-dependent skeletal muscle myopathy associated with myofibrillar and intermyofibrillar disorganization in mice.Human molecular genetics · 2014Article
- Proteomic profiling of halloysite clay nanotube exposure in intestinal cell co-culture.Journal of applied toxicology : JAT · 2013Article
- Bioinformatic Analysis of Differential Protein Expression in Calu-3 Cells Exposed to Carbon Nanotubes.Proteomes · 2013Article
- Perivascular adipose tissue potentiates contraction of coronary vascular smooth muscle: influence of obesity.Circulation · 2013Article
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Authors and funding
4 authors.
Funding
Abstract
Though many software packages have been developed to perform label-free quantification of proteins in complex biological samples using peptide intensities generated by LC-MS/MS, two critical issues are generally ignored in this field: (i) peptides have multiple elution patterns across runs in an experiment, and (ii) many peptides cannot be used for protein quantification. To address these two key issues, we have developed a novel alignment method to enable accurate peptide peak retention time determination and multiple filters to eliminate unqualified peptides for protein quantification. Repeatability and linearity have been tested using six very different samples, i.e., standard peptides, kidney tissue lysates, HT29-MTX cell lysates, depleted human serum, human serum albumin-bound proteins, and standard proteins spiked in kidney tissue lysates. At least 90.8% of the proteins (up to 1,390) had CVs ≤ 30% across 10 technical replicates, and at least 93.6% (up to 2,013) had R(2) ≥ 0.9500 across 7 concentrations. Identical amounts of standard protein spiked in complex biological samples achieved a CV of 8.6% across eight injections of two groups. Further assessment was made by comparing mass spectrometric results to immunodetection, and consistent results were obtained. The new approach has novel and specific features enabling accurate label-free quantification.
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