Proteomic profiling of human urine using multi-dimensional protein identification technology

Ru, Qinhua; Katenhusen, Richard; Zhu, Luwang Andy; Silberman, Jordan; Song, Yang; Orchard, Trevor J.; Brzeski, Henry; Liebman, Michael; Ellsworth, Darrell L.

doi:10.1016/j.chroma.2005.06.081

Cited by 33 publications

(18 citation statements)

References 13 publications

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“…24 Most recently, Ru et al used multidimensional protein identification technology (MudPIT) to identify 87 proteins in human urine. 25 It is interesting to note that no more than 30 mL of urine was needed in our experiments while hundreds of milliliters of urine is typically used for gel-based analysis. [16][17][18][19]23 The pooling of samples from different individuals is typically observed in the published gel analysis of urines to increase the amount of proteins.…”

Section: Discussionmentioning

confidence: 99%

Bladder Cancer Associated Glycoprotein Signatures Revealed by Urinary Proteomic Profiling

et al. 2007

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Current methods in the noninvasive detection and surveillance of bladder cancer via urine analysis include voided urine cytology (VUC) and some diagnostic urinary protein biomarkers; however, due to the poor sensitivity of VUC and high false-positive rates of currently available protein assays, detection of bladder cancer via urinalysis remains a challenge. In the study presented here, a rapid, high-sensitivity technique was developed to profile the N-linked glycoprotein component in naturally micturated human urine specimens. Concanavalin A (Con A) affinity chromatography coupled to nanoflow liquid chromatography was utilized to separate the complex peptide mixture prior to a linear ion trap MS analysis. Of 186 proteins identified with high confidence by multiple analyses, 40% were secreted proteins, 18% membrane proteins, and 14% extracellular proteins. In this study, the presence of several proteins appeared to be associated with the presence of bladder cancer, including R-1B-glycoprotein that was detected in all tumor-bearing patient samples but in none of the samples obtained from nontumor-bearing individuals. The combination of Con A affinity chromatography and nano-LC/MS/MS provides an initial investigation of N-glycoproteins in complex biological samples and facilitates the identification of potential biomarkers of bladder cancer in noninvasively obtained human urine.

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Section: Discussionmentioning

confidence: 99%

Bladder Cancer Associated Glycoprotein Signatures Revealed by Urinary Proteomic Profiling

et al. 2007

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“…There have been several recent studies of the total human urinary proteome [3,21,[24][25][26][27][28][29] and the greatest number of the Man-6-P containing lysosomal proteins (40 proteins in total; Online Supplementary Data Table 1) was identified by Adachi et al [3]. Only two lysosomal proteins that are known to contain Man-6-P (GM2A activator protein and galactocerebrosidase) were identified in one or more of the previous studies but not found in this present study.…”

Section: Resultsmentioning

confidence: 99%

The human urine mannose 6-phosphate glycoproteome

Sleat¹,

Zheng²,

Lobel³

2007

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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Glycoproteins containing the mannose 6-phosphate (Man-6-P) modification represent a class of proteins of considerable biomedical importance. They include over sixty different soluble lysosomal hydrolases and accessory proteins, deficiencies of which result in over forty different known human genetic diseases. In addition, there are patients with lysosomal storage diseases of unknown etiology and lysosomal proteins have been implicated in pathophysiological processes associated with Alzheimer disease, arthritis, and cancer. The aim of this study was to explore urine as a source for the proteomic investigation of lysosomal storage disorders as well as for biomarker studies on the role of Man-6-P containing proteins in other human diseases. To this end, urinary proteins were affinity purified on immobilized Man-6-P receptors, digested with trypsin, and analyzed using nanospray LC/MS/MS. This resulted in identification of 67 proteins, including 48 known lysosomal proteins and 9 proteins that may be lysosomal. The identification of a large proportion of the known set of soluble lysosomal proteins with relatively few contaminants suggests that urine represents a promising substrate for the development of comparative proteomic methods for the investigation of lysosomal disorders and other diseases involving Man-6-P glycoproteins.

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“…A sequential separation using different media in two independent steps provides a multidimensional fractionation that can generate vast amounts of information. For example, the multidimensional protein identification technology (MudPIT) (27,28) and a 2D liquid-phase fractionation approach (29) are well suited for an in-depth analysis of body fluids and tissues ( Figure 3). Limitations of LC-MS include difficulties with comparative analysis, in part because of the variability in multidimensional separations and the substantial time required for the analysis of a single sample (generally, in days).…”

Section: Liquid Chromatography Coupled To Mass Spectrometrymentioning

confidence: 99%

Advances in Urinary Proteome Analysis and Biomarker Discovery

Fliser¹,

Novák²,

Thongboonkerd³

et al. 2007

Journal of the American Society of Nephrology

256

206

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Noninvasive diagnosis of kidney diseases and assessment of the prognosis are still challenges in clinical nephrology. Definition of biomarkers on the basis of proteome analysis, especially of the urine, has advanced recently and may provide new tools to solve those challenges. This article highlights the most promising technological approaches toward deciphering the human proteome and applications of the knowledge in clinical nephrology, with emphasis on the urinary proteome. The data in the current literature indicate that although a thorough investigation of the entire urinary proteome is still a distant goal, clinical applications are already available. Progress in the analysis of human proteome in health and disease will depend more on the standardization of data and availability of suitable bioinformatics and software solutions than on new technological advances. It is predicted that proteomics will play an important role in clinical nephrology in the very near future and that this progress will require interactive dialogue and collaboration between clinicians and analytical specialists.

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Proteomic profiling of human urine using multi-dimensional protein identification technology

Cited by 33 publications

References 13 publications

Bladder Cancer Associated Glycoprotein Signatures Revealed by Urinary Proteomic Profiling

Bladder Cancer Associated Glycoprotein Signatures Revealed by Urinary Proteomic Profiling

The human urine mannose 6-phosphate glycoproteome

Advances in Urinary Proteome Analysis and Biomarker Discovery

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