Mass Spectrometry-Based Label-Free Quantitative Proteomics

Zhu, Wenhong; Smith, Jeffrey W.; Huang, Chun Ming

doi:10.1155/2010/840518

Cited by 488 publications

(464 citation statements)

References 42 publications

(48 reference statements)

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“…Normalized peptide counts were used as a semiquantitative measurement of relative protein abundance. Validation of this approach has been previously published (32,33). Peptide counts were normalized by dividing the number of peptides observed for a given protein by the total number of peptides observed in a sample.…”

Section: Methodsmentioning

confidence: 99%

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

Carlson

Clark²,

Blazewicz³

et al. 2013

Journal of Bacteriology

155

160

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Phylogenetically diverse species of bacteria can catalyze the oxidation of ferrous iron [Fe(II)] coupled to nitrate (NO 3؊ ) reduction, often referred to as nitrate-dependent iron oxidation (NDFO). Very little is known about the biochemistry of NDFO, and though growth benefits have been observed, mineral encrustations and nitrite accumulation likely limit growth. Acidovorax ebreus, like other species in the Acidovorax genus, is proficient at catalyzing NDFO. Our results suggest that the induction of specific Fe(II) oxidoreductase proteins is not required for NDFO. No upregulated periplasmic or outer membrane redox-active proteins, like those involved in Fe(II) oxidation by acidophilic iron oxidizers or anaerobic photoferrotrophs, were observed in proteomic experiments. We demonstrate that while "abiotic" extracellular reactions between Fe(II) and biogenic NO 2 ؊ /NO can be involved in NDFO, intracellular reactions between Fe(II) and periplasmic components are essential to initiate extensive NDFO. We present evidence that an organic cosubstrate inhibits NDFO, likely by keeping periplasmic enzymes in their reduced state, stimulating metal efflux pumping, or both, and that growth during NDFO relies on the capacity of a nitrate-reducing bacterium to overcome the toxicity of Fe(II) and reactive nitrogen species. On the basis of our data and evidence in the literature, we postulate that all respiratory nitrate-reducing bacteria are innately capable of catalyzing NDFO. Our findings have implications for a mechanistic understanding of NDFO, the biogeochemical controls on anaerobic Fe(II) oxidation, and the production of NO 2 ؊ , NO, and N 2 O in the environment.

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Section: Methodsmentioning

confidence: 99%

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

Carlson

Clark²,

Blazewicz³

et al. 2013

Journal of Bacteriology

155

160

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show abstract

“…Among all strategies used for quantitative proteomics (Thelen and Peck, 2007;van Wijk and Baginsky, 2011) we followed a label-free option of spectral counting (Liu et al, 2004;Booth et al, 2011) described in Bouyssié et al (2007). The spectral-count-based label free has been reported as allowing quantification of protein abundance with similar efficiency to isotope labeling (Zhu et al, 2009). This methodology had been applied in a number of other studies related to the plastid proteome (Bräutigam et al, 2008;Ferro et al, 2010;Demartini et al, 2011).…”

Section: Trypsin Digestion and Liquid Chromatography Ms/ms Analyses Omentioning

confidence: 99%

Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components

et al. 2012

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A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato (Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration) and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome.

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“…Thus, investigators are progressively switching to label-free quantitative proteomic methods given their lower costs, higher dynamic range of quantification, and faster results (Mann, 2009;Patel et al, 2009). MS-based, label-free quantitative proteomics embraces two general categories (Zhu et al, 2010): ion abundancebased measurements (peptide peak areas or peak heights) and spectral counting of identified proteins after MS/MS analysis. Compared with labeling approaches, these methods have to be carefully controlled given the possible errors caused by run-torun variations when performing LC and MS.…”

Section: Proteomic Studies In Micementioning

confidence: 99%

Proteomic Approaches and Identification of Novel Therapeutic Targets for Alcoholism

Gorini

Harris

Mayfield

2013

Neuropsychopharmacol

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Recent studies have shown that gene regulation is far more complex than previously believed and does not completely explain changes at the protein level. Therefore, the direct study of the proteome, considerably different in both complexity and dynamicity to the genome/transcriptome, has provided unique insights to an increasing number of researchers. During the past decade, extraordinary advances in proteomic techniques have changed the way we can analyze the composition, regulation, and function of protein complexes and pathways underlying altered neurobiological conditions. When combined with complementary approaches, these advances provide the contextual information for decoding large data sets into meaningful biologically adaptive processes. Neuroproteomics offers potential breakthroughs in the field of alcohol research by leading to a deeper understanding of how alcohol globally affects protein structure, function, interactions, and networks. The wealth of information gained from these advances can help pinpoint relevant biomarkers for early diagnosis and improved prognosis of alcoholism and identify future pharmacological targets for the treatment of this addiction.

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Mass Spectrometry-Based Label-Free Quantitative Proteomics

Cited by 488 publications

References 42 publications

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components

Proteomic Approaches and Identification of Novel Therapeutic Targets for Alcoholism

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