Proteomics is one of the most important functional genomics research in the post-genomic era, which is closely related to medical biology, chemistry, physics, information science and modern technology. Through review research progress of some important proteomics, a proteomics special issue is published so as to find problems, explore the possible applications and outlook the development prospects of proteomics. The special issue consists of reviews and original papers, mainly involving in the following aspects, i) proteomics about different species such as humans, mammals, prokaryotes and actinobacterial; ii) proteomics methodology and techniques including tandem mass spectrometry analysis, film (urimem) preservation of urine protein, quantitative proteomic analysis and meta analysis; iii) function and application of proteome such as spider (Latrodectus tredecimguttatus) toxins proteome, protein phosphorylation proteome, oocytes and early embryos proteomes, liver fibrosis proteome, drug-resistant mycobacterium tuberculosis proteome, etc.
Animals ; Humans ; Proteome ; Proteomics ; Tandem Mass Spectrometry

Objective To screen early urine protein markers for minimal change nephropathy.Methods Adriamycin nephropathy was employed as minimal change nephropathy model.Urinary protein and ConA captured glycoproteins were respectively profiled.Results By profiling urine proteome,25 differential proteins were identified.These differential proteins were from leaked plasma proteins,secreted proteins from immuno-and inflammatory cells,specifically asecreted proteins from urinary tract,and so on.They took part in different pathogenic process,eg.hemodynamic changes,podocytes injury,immunological disorder and so on.By profiling ConA-enriched urinary glycoproteome,21 differential proteins were identified,among which 12(57%) were different from the above 25 differential proteins.This indicates that the knowledge of urine glycoproteome is complementary to urine proteome in understanding kidney condition.Conclusion These differential proteins can be potential indicators of minimal change nephropathy,and can help better understand the pathogenesis by further studying their functions.

The preservation of urinary proteins on a membrane plays a vital role in biomarker research, and the efficient elution of proteins preserved on nitrocellulose membrane (NC membrane) determines the application of this method. During the heating elution procedure, we raised the temperature to reduce the intense vortexing time, and kept gentle rotating while precipitation to prevent nitrocellulose reformation. We also used SDS-PAGE and LC-MS/MS to analyze the urinary proteins prepared by heating elution procedure, intense vortexing elution procedure and acetone precipitation method. There was no degradation of proteins prepared by heating elution procedure. Compared with proteins prepared by heating elution method and acetone precipitation method, the overlapping rates of the proteins was almost the same (92.6% versus 96.8%) and the ratios of CV values (< 20%) of the proteins were both high (85.2% and 94.4%). The heating elution procedure achieved good technical reproducibility, and was much simpler and more efficient than the previous one. It can facilitate the application of the preservation of urinary proteins on membrane.
Acetone ; Biomarkers ; urine ; Chromatography, Liquid ; Collodion ; Electrophoresis, Polyacrylamide Gel ; Hot Temperature ; Humans ; Proteins ; isolation & purification ; Reproducibility of Results ; Tandem Mass Spectrometry ; Urine ; chemistry

As one of the important areas in proteomics,glycoproteome is in the spotlight currently.In this paper,the description of glycoproteins,the enrichment methods of glycoproteins/glycopeptides,the identification approaches of glycoproteins/glycopeptides and the application of glycoproteome were overviewed.

Nitrocellulose membrane based urinary protein preservation method is simple, fast and economic, but its advantage over the traditionally used acetone precipitation method is still unclear. In this work, we prepared urinary proteins by the two methods by LC-MS/MS. Then we used protein spectra counts to assess the reproducibility of the two methods. Proteins identified by the two methods were almost the same in number, spectral count distribution and distribution of coefficients of variation value. In conclusion, nitrocellulose membrane method is generally the same as acetone precipitation method. It can be used for large scale preservation of clinical urine samples.
Acetone ; Chromatography, Liquid ; Collodion ; Humans ; Mass Spectrometry ; Proteins ; isolation & purification ; Reproducibility of Results ; Tandem Mass Spectrometry ; Urine ; chemistry

The main objective of today’s graduate education reform is to improve the quality of graduate students. Curriculum development, as an essential part of graduate education, is pivotal to this goal. While classroom teaching innovation is placed in the front of curriculum development, it has become an important issue for graduate education study to practice an alternative capability centered way other than the current knowledge centered classroom teaching. We offered the course called "literature presentation and discussion" to the class 2006 graduate students at Chinese Academy of Medical Sciences. This article briefed and discussed the purpose,practice of this course,feedbacks from students and problems and solutions.

Objective To investigate the ligand-binging characteristics of Veli3 PDZ.Methods Random peptide library was screened using yeast two-hybrid method with Veli3 PDZ as bait.In combination with bioinformatics method all the potential ligands in human proteome were predicted by searching human databases with the consensus-binding sequences.Fourteen native human proteins predicted as ligands were chosen by their cellular locations and biological functions for validating protein interaction in yeast two-hybrid system.Results The C-terminal consensus sequences for the Veil3 PDZ binding is X-COOH(X denotes any amino acid),which indicates that Veli3 PDZ belongs to classⅠ.Six of fourteen native human proteins predicted as ligands were confirmed to be positive in the yeast two-hybrid system.There were a lot of interactions between PSD-95,another PDZ protein,and the ligands of Veli3 PDZ reported previously and discovered in this study.Conclusion The six novel potential ligands of Veli3 found in this study provide significant clues for discovering biological functions of Veil3 proteins.Moreover,Veli3 PDZ and PSD-95 PDZ may compete in binding the same ligands.

ObjectiveTo establish the urinary proteome profile of the metabolic syndrome ( MetS ) patients,compare the different urinary proteins between the MetS patients and the normal individuals,and analyze the function of the different proteins,so as to explore the pathogenesis of MetS.MethodsOvernight urine were collected from normal controls (n =6) and MetS patients ( n =6).Acetone precipitation method was used to precipitate proteins of urine.Intra-group proteins were mixed together,identified by reversed phase liquid chromatography-mass spectrometry/mass spectrometry and quantified relatively using spectral counting method.The functions of differential proteins were analyzed using Panther.ResultsA total of 807 and 630 proteins were identified respectively in normal controls and MetS patients.Comparing MetS patients with normal controls,sixty different proteins were found,of which 23 proteins were up-regulated and 37 proteins were down-regulated in MetS patients.In the up-regulated proteins,plasminogen was involved in the plasminogen activation cascade and isoform of alphaenolase,phosphoglycerate kinase 1 and fructose-bisphosphate aldolase B down-regulated in MetS patients were involved in the process of glycolysis and fructose metabolism.ConclusionsThe urinary proteome profile of patients with MetS was established by reversed phase liquid chromatography-mass spectrometry/mass spectrometry.Different proteins between MetS patients and normal people were identified.The plasminogen activation cascade,glycolysis and fructose metabolism play key roles in the pathogenesis of MetS.

To compare two enrichment and preservation methods of urinary proteins, stored in polyvinylidene difluoride (PVDF) membrane (Urimem) or direct freezing, we examined the differences between the two methods in time, space, costs of supplies and electricity, degree of protein degradation and convenience of the sample handling. The urimem method is superior in the storage space, the cost of electricity and the clinical convenience compared to the direct freezing method. However, the direct freezing method is superior in the time and the cost of supplies to the urimem method. The enrichment and preservation of urinary proteins using urimem have more cost-effective benefits compared to those of the direct freezing method.
Cost-Benefit Analysis ; Freezing ; Humans ; Polyvinyls ; Preservation, Biological ; methods ; Proteins ; chemistry ; Urine ; chemistry

Biomarker is the measurable change associated with a physiological or pathophysiolog-ical process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F;hydro-chlorothiazide, H; and spirolactone, S) on the urinary proteome in rats. Urine samples were col-lected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Based on the criteria of P 6 0.05, a fold change P2, a spectral count P5, and false positive rate (FDR) 61%, 14 proteins (seven for F, five for H, and two for S) were identified by Progenesis LC-MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics.