Reference map for liquid chromatography–mass spectrometry-based quantitative proteomics

Kim, Yeoun Jin; Feild, Brian; Fitzhugh, William W.; Heidbrink, Jenny L.; Duff, J. W.; Heil, Jeremy; Ruben, Steven M.; He, Tao

doi:10.1016/j.ab.2009.06.015

Cited by 12 publications

(8 citation statements)

References 24 publications

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“…S1). They illustrate that a two-tiered workflow consisting of (a) an "accurate mass and time tag" approach for initial global profiling (20,38,(51)(52)(53) in combination with (b) targeted LFQ of particular proteins of interest based on scheduled precursor lists and alternating MS and MS/MS acquisition (39) improves label-free quantitation accuracy. Although the additional targeted LFQ step is time-consuming when applied to a large number of proteins it offers similar advantages as other targeted approaches such as selected reaction monitoring (SRM) (54).…”

Section: Discussionmentioning

confidence: 99%

“…Global Quantitative Profiling-Global quantitative profiling was performed using ProfileAnalysis 2.0 and Proteinscape 3.1 (Bruker Daltonics) according to the "accurate mass and time tag" approach (38). Quantitative global profiling ratios (salinity stress versus handling controls) for identified proteins have been deposited along with the corresponding protein identification and mass spectrometry data in the PRIDE repository (29) and are available under PRIDE accession numbers 28622-28631.…”

Section: Methodsmentioning

confidence: 99%

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Quantitative Molecular Phenotyping of Gill Remodeling in a Cichlid Fish Responding to Salinity Stress

Kültz

Gardell

et al. 2013

Molecular & Cellular Proteomics

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A two-tiered label-free quantitative (LFQ) proteomics workflow was used to elucidate how salinity affects the molecular phenotype, i.e. proteome, of gills from a cichlid fish, the euryhaline tilapia (Oreochromis mossambicus). The workflow consists of initial global profiling of relative tryptic peptide abundances in treated versus control samples followed by targeted identification (by MS/MS) and quantitation (by chromatographic peak area integration) of validated peptides for each protein of interest. Fresh water acclimated tilapia were independently exposed in separate experiments to acute short-term (34 ppt) and gradual long-term (70 ppt, 90 ppt) salinity stress followed by molecular phenotyping of the gill proteome. The severity of salinity stress can be deduced with high technical reproducibility from the initial global label-free quantitative profiling step alone at both peptide and protein levels. However, an accurate regulation ratio can only be determined by targeted label-free quantitative profiling because not all peptides used for protein identification are also valid for quantitation. Of the three salinity challenges, gradual acclimation to 90 ppt has the most pronounced effect on gill molecular phenotype. Known salinity effects on tilapia gills, including an increase in the size and number of mitochondria-rich ionocytes, activities of specific ion transporters, and induction of specific molecular chaperones are reflected in the regulation of abundances of the corresponding proteins. Moreover, specific protein isoforms that are responsive to environmental salinity change are resolved and it is revealed that salinity effects on the mitochondrial proteome are nonuniform. Furthermore, protein NDRG1 has been identified as a novel key component of molecular phenotype restructuring during salinity-induced gill remodeling. In conclusion, besides confirming known effects of salinity on gills of euryhaline fish, molecular phenotyping reveals novel insight into proteome changes that underlie the remodeling of tilapia gill epithelium in response to environmental salinity change. Molecular & Cellular Proteomics 12: 10.1074/ mcp.M113.029827, 3962-3975, 2013.Euryhaline fish are capable of living in fresh water (FW), 1 brackish water (BW), seawater (SW), and hypersaline water (ϾSW). They adjust transepithelial ion transport across gill epithelium when challenged by an environmental salinity change (1). Acclimation from hyposmotic (relative to plasma, e.g. FW) to hyperosmotic (relative to plasma, e.g. SW) environments is accompanied by extensive remodeling of gill epithelium, the most prominent feature of which is an increase in the number and size of salt-secretory, mitochondria-rich ionocytes (2). In addition, molecular chaperones and distinct sets of transport proteins are activated when euryhaline fish are challenged by increasing environmental salinity (3)(4)(5). A euryhaline fish species in which these physiological responses have been observed is the Mozambique tilapia, Oreochromis mossambicus (6 -8). Tilapi...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Quantitative Molecular Phenotyping of Gill Remodeling in a Cichlid Fish Responding to Salinity Stress

Kültz

Gardell

et al. 2013

Molecular & Cellular Proteomics

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“…Consequently, many investigators now feel that the proteome may contain the most highly informative biomarkers for the detection of aggressive prostate cancer and patient-tailored therapy once the disease is detected. The current landscape of high-throughput proteomic technologies is constantly advancing (30)(31)(32)(33)(34)(35)(36)(37)(38) and now offers the possibility to evaluate, in a single experimental step, the abundance, expression, and activation state of hundreds of proteins in tissues and biological fluids, allowing a complete overview of the complex events that underpin tumor development and progression. Such information will help in better molecular characterization of the tumor and in the identification of more specific tumor biomarkers that could be directly transferred to clinical practices once extensive validation has been performed.…”

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confidence: 99%

Application of proteomic technologies for prostate cancer detection, prognosis, and tailored therapy

Fredolini

Liotta

Petricoin

2010

Critical Reviews in Clinical Laboratory Sciences

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Prostate cancer affects 3 in 10 men over the age of 50 years, and, unfortunately, the clinical course of the disease is poorly predicted. At present, there is no means that can distinguish indolent from aggressive/metastatic tumors. Thus, a personalized clinical approach could be helpful in diagnosing clinically relevant disease and guiding appropriate patient therapy. Individualized medicine requires a deep knowledge of the molecular mechanisms underpinning prostate cancer carcinogenesis. Proteomics may be the most powerful way to uncover biomarkers of detection, prognosis, and prediction, as proteins do the work of the cell and represent the majority of the diagnostic markers and drug targets today. Proteomic technologies are rapidly advancing beyond the two-dimensional gel separation techniques of the past to new types of mass spectrometry and protein microarray analyses. Biological fluids and tissue-cell proteomes from men with prostate cancer are being explored to identify diagnostic and prognostic biomarkers and therapeutic targets using these new proteomic approaches. Traditional and novel proteomic technology and their application to prostate cancer studies in translational research will be presented and discussed in this review. Proteomics coupled with powerful nanotechnology-based biomarker discovery approaches may provide a new and exciting opportunity for body fluid-borne biomarker discovery and characterization. While innovative mass spectrometry technology and nanotrap could be applied to improve the discovery and measurement of biomarkers for the early detection of prostate cancer, the use of tissue proteomic tools such as the reverse-phase protein microarray may provide new approaches for personalization of therapies tailored to each tumor's unique pathway activation network.

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“…Recently, a new label-free quantitative technique based on liquid chromatography coupling with tandem mass spectrometry was proposed, and has been recommended by more and more researchers (8,13,15). The label-free quantitative technique can also be divided into two classes: a technique based on MS information and based on MS/MS information.…”

Section: Introductionmentioning

confidence: 99%

A Label-Free Strategy for both Qualification and Quantitation of Protein Based on Tandem Mass Spectrometry

Wang

Zhao

Liu

et al. 2012

Biotechnology & Biotechnological Equipment

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Reference map for liquid chromatography–mass spectrometry-based quantitative proteomics

Cited by 12 publications

References 24 publications

Quantitative Molecular Phenotyping of Gill Remodeling in a Cichlid Fish Responding to Salinity Stress

Quantitative Molecular Phenotyping of Gill Remodeling in a Cichlid Fish Responding to Salinity Stress

Application of proteomic technologies for prostate cancer detection, prognosis, and tailored therapy

A Label-Free Strategy for both Qualification and Quantitation of Protein Based on Tandem Mass Spectrometry

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