Mass Spectrometry Based Strategies in Quantitative Proteomics

Brancia, Francesco L.

doi:10.2174/157341106775197367

Cited by 7 publications

(5 citation statements)

References 51 publications

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“…However, differences in protein expression in clinical studies and their correlation to the disease are the main focus of interest [ 5 ]. Quantitative proteomic methods, like isobaric tag labeling, provide information about relative protein concentrations [ 6 , 7 ] and also allow for multiplexed approaches.…”

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis

Füvesi

Hanrieder

Bencsik

et al. 2012

IJMS

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Multiple Sclerosis (MS) is a chronic disease, but in rare fulminant cases rapid progression may lead to death shortly after diagnosis. Currently there is no diagnostic test to predict disease course. The aim of this study was to identify potential biomarkers/proteins related to rapid progression. We present the case history of a 15-year-old male MS patient. Cerebrospinal fluid (CSF) was taken at diagnosis and at the time of rapid progression leading to the patient’s death. Using isobaric tag labeling and nanoflow liquid chromatography in conjunction with matrix assisted laser desorption/ionization time of flight tandem mass spectrometry we quantitatively analyzed the protein content of two CSF samples from the patient with fulminant MS as well as one relapsing-remitting (RR) MS patient and one control headache patient, whose CSF analysis was normal. Seventy-eight proteins were identified and seven proteins were found to be more abundant in both fulminant MS samples but not in the RR MS sample compared to the control. These proteins are involved in the immune response, blood coagulation, cell proliferation and cell adhesion. In conclusion, in this pilot study we were able to show differences in the CSF proteome of a rapidly progressing MS patient compared to a more typical clinical form of MS and a control subject.

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Section: Introductionmentioning

confidence: 99%

Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis

Füvesi

Hanrieder

Bencsik

et al. 2012

IJMS

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“…Quantitative proteomics, the study of global changes in protein expression, is a rapidly growing field where two-dimensional (2D) 1 gel electrophoresis (1,2), differential labeling of protein and peptides with stable isotopes (3), and label-free mass spectrometric peak intensity measurements (4) are pivotal approaches to measuring changes in the expression level of proteins. The output of large scale genomic sequencing and gene expression studies have driven the need to globally assess protein behavior, which is central to our understanding of cellular function and disease processes.…”

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confidence: 99%

Experimental and Statistical Considerations to Avoid False Conclusions in Proteomics Studies Using Differential In-gel Electrophoresis

Karp

McCormick²,

Russell

et al. 2007

Molecular & Cellular Proteomics

152

137

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In quantitative proteomics, the false discovery rate (FDR) can be defined as the number of false positives within statistically significant changes in expression. False positives accumulate during the simultaneous testing of expression changes across hundreds or thousands of protein or peptide species when univariate tests such as the Student's t test are used. Currently most researchers rely solely on the estimation of p values and a significance threshold, but this approach may result in false positives because it does not account for the multiple testing effect. For each species, a measure of significance in terms of the FDR can be calculated, producing individual q values. The q value maintains power by allowing the investigator to achieve an acceptable level of true or false positives within the calls of significance. The q value approach relies on the use of the correct statistical test for the experimental design. In this situation, a uniform p value frequency distribution when there are no differences in expression between two samples should be obtained. Here we report a bias in p value distribution in the case of a three-dye DIGE experiment where no changes in expression are occurring. The bias was shown to arise from correlation in the data from the use of a common internal standard. With a two-dye schema, where each sample has its own internal standard, such bias was removed, enabling the application of the q value to two different proteomics studies. In the case of the first study, we demonstrate that 80% of calls of significance by the more traditional method are false positives. In the second, we show that calculating the q value gives the user control over the FDR. These studies demonstrate the power and ease of use of the q value in correcting for multiple testing. This work also highlights the need for robust experimental design that includes the appropriate application of statistical procedures. Molecular & Cellular Proteomics 6: 1354 -1364, 2007.Quantitative proteomics, the study of global changes in protein expression, is a rapidly growing field where two-dimensional (2D) 1 gel electrophoresis (1, 2), differential labeling of protein and peptides with stable isotopes (3), and label-free mass spectrometric peak intensity measurements (4) are pivotal approaches to measuring changes in the expression level of proteins. The output of large scale genomic sequencing and gene expression studies have driven the need to globally assess protein behavior, which is central to our understanding of cellular function and disease processes. In quantitative studies, the quantitation of the protein or peptide signal allows the comparison of protein levels from one state with another. Regardless of the technique used, the data generated can be analyzed with a variety of statistical approaches. In a simple comparison of two samples, changes in protein expression are considered to be significant when above a specified threshold (5). More rigorous studies incorporating replicates use univariate (1, 6) or multivari...

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“…Quantitative proteomic methods, like, e.g. isobaric tag labeling, provide information on relative protein concentrations and allow temporally resolved monitoring of protein expression profiles in biological samples (Brancia, 2006;Ross et al, 2004). Several protein upand down-regulations after TBI and their correlation to the severity of the injury as well as patients outcome have already been reported and evaluated in previous studies (Conti et al, 2004;Haskins et al, 2005;Jenkins et al, 2002;Kobeissy et al, 2006;Ottens et al, 2005;Pike et al, 2001;Raabe et al, 1999;Wang et al, , 2005.…”

Section: Introductionmentioning

confidence: 99%

Temporally resolved differential proteomic analysis of human ventricular CSF for monitoring traumatic brain injury biomarker candidates

Hanrieder¹,

Wetterhall²,

Enblad³

et al. 2009

Journal of Neuroscience Methods

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Mass Spectrometry Based Strategies in Quantitative Proteomics

Cited by 7 publications

References 51 publications

Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis

Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis

Experimental and Statistical Considerations to Avoid False Conclusions in Proteomics Studies Using Differential In-gel Electrophoresis

Temporally resolved differential proteomic analysis of human ventricular CSF for monitoring traumatic brain injury biomarker candidates

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