To date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries. Here we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration. Our results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol.

Affinity depletion of abundant proteins from human plasma has become a routine sample preparation strategy in proteomics used prior to protein identification and quantitation. To date, there have been limited published studies comparing the performance of commercially available depletion products. We conducted a thorough evaluation of six depletion columns using 2-DE combined with sophisticated image analysis software, examining the following criteria:(i) efficiency of high-abundance protein depletion,(ii) non-specific removal of other than the targeted proteins and (iii) total number of protein spots detected on the gels following depletion. From all the products investigated, the Seppro IgY system provided the best results. It displayed the greatest number of protein spots on the depleted plasma gels, minimal non-specific binding and high efficiency of abundant protein removal. Nevertheless, the increase in the number of detected spots compared with the second best performing and cheaper multiple affinity removal column (MARC) was not shown to be statistically significant. The ProteoPrep spin column, considered to be the "deepest" depletion technique available at the time of conducting the study, surprisingly displayed significantly fewer spots on the flow-through fraction gels compared with both the Seppro and the MARC. The spin column format and low plasma capacity were also found to be impractical for 2-DE. To conclude, we succeeded in providing an overview of the depletion columns performances with regard to the three examined areas. Our study will serve as a reference to other scientists when deciding on the optimal product for their particular projects.

BACKGROUND Primary focal segmental glomerulosclerosis (FSGS) is a glomerular disease that frequently does not respond to treatment and progresses to kidney failure. FSGS can be of either genetic origin, caused by mutations in slit diaphragm proteins, such as podocin, or idiopathic origin of unknown cause. STUDY DESIGN Case series. SETTING & PARTICIPANTS Children with FSGS (aged 3-18 years); 15 with idiopathic and 11 with genetic forms of FSGS. PREDICTOR Genetic versus idiopathic forms. OUTCOMES & MEASUREMENTS Differentially expressed proteins in the plasma proteome, detected using 2-dimensional electrophoresis and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Western blot, and liquid chromatography electron spray ionization tandem mass spectrometry for fragmentation and identification of the peptides. RESULTS We found 3 very low-molecular-mass (9.2, 6.9, and 4.7 kDa; isoelectric point, 5.7) spots that were present in pooled samples from patients with genetic FSGS, but missing in patients with idiopathic FSGS and healthy individuals. Spots were identified using mass spectrometry as fragments of albumin, 2 of them apparently containing peptides from both C- and N-terminal parts of the whole protein. Proteomic analyses were carried out on all genetic patients individually; of these, 10 of 11 patients had > or =1 albumin fragment detected in the pool. We did not find an evident relationship between type of mutation or clinical status of patients and albumin fragments observed. LIMITATIONS Very low-molecular-weight albumin fragments also can be produced by other diseases. CONCLUSIONS We describe for the first time the presence of very low-molecular-mass albumin fragments in plasma of patients with FSGS with podocyte protein mutations that are absent in patients with idiopathic FSGS or healthy individuals. Additional studies are necessary to determine whether these fragments could be potential biomarkers to distinguish between genetic and idiopathic forms of FSGS.

SUMMARY: The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network. It provides references to the CORUM, DrugBank, KEGG, and Reactome pathway databases. DICS can be accessed for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby pro-viding valuable information about the functional context. AVAILABILITY: http://mips.gsf.de/proj/dics SUPPLEMENTARY INFORMATION: Supplementary information on data sets and methods is available on the web-server. CONTACT: sabine.dietmann@googlemail.com.

In 1981-1982, individuals in fourteen central and northwest provinces in Spain were affected by an illness that was eventually labeled toxic oil syndrome (TOS) by the World Health Organization. Thousands of individuals were diagnosed with, and 356 people eventually died from, the disease. The disease shares striking similarities with several autoimmune diseases, particularly eosinophilia-myalgia syndrome (EMS) and diffuse fasciitis with eosinophilia (DFE). As with many other autoimmune diseases, women were more severely affected than men and made up a significant portion of TOS-related deaths. While a number of etiologic agents were investigated, disease occurrence was found to be significantly associated with consumption of contaminated rapeseed oil produced by a particular refinery. Two compounds, 1,2-di-oleyl ester (DEPAP) and oleic anilide are considered to be biologically relevant contaminants that may contribute to disease development. Toxic oil syndrome was a three-phase disease with an initial non-necrotizing vasculitis in multiple organs. Suspected immune mechanisms in TOS include activation of T-cells, altered cytokine production, and several studies have associated disease severity with HLA-DR2 and polymorphisms in metabolism and immune response genes. While a number of animal models have been used to investigate the underlying immune mechanisms in TOS, only a few studies in rodents have demonstrated the classical symptoms of TOS. Biotransformation and oxidation of the parent compound(s) to reactive intermediates prior to induction of autoreactive pathways appears to be an important component of the disease process. These reactive intermediates could haptenate self-proteins and activate autoreactive T-cells, disrupt signal transduction, or induce apoptosis and necrosis to release abnormal forms of self-antigens. Although the TOS epidemic was limited to a discrete period of time, the origin of the contamination determined, and the spread of the disease halted by government intervention, the underlying immune mechanisms have yet to be elucidated.

Nasopharyngeal carcinoma (NPC), one of the most common cancers in population with Chinese or Asian progeny, poses a serious health problem for southern China. It is unfortunate that most NPC victims have had lymph node metastasis (LNM) when first diagnosed. We believe that the 2D based serum proteome analysis can be useful in discovering new biomarkers that may aid in the diagnosis and therapy of NPC patients. To filter the tumor specific antigen markers of NPC, sera from 42 healthy volunteers, 27 non-LNM NPC patients and 37 LNM NPC patients were selected for screening study using 2D combined with MS. Pretreatment strategy, including sonication, albumin and immunoglobulin G (IgG) depletion, was adopted for screening differentially expressed proteins of low abundance in serum. By 2D image analysis and MALDI-TOF-MS identification, twenty-three protein spots were differentially expressed. Three of them were further validated in the sera using enzyme-linked immunosorbent assay (ELISA). Our research demonstrates that HSP70, sICAM-1 and SAA, confirmed with ELISA at sera and immunohistochemistry, are potential NPC metastasis-specific serum biomarkers which may be of great underlying significance in clinical detection and management of NPC.

BACKGROUND Despite its widespread use to assess fibrosis, liver biopsy has several important drawbacks, including that is it semi-quantitative, invasive, and limited by sampling and observer variability. Non-invasive serum biomarkers may more accurately reflect the fibrogenetic process. To identify potential biomarkers of fibrosis, we compared serum protein expression profiles in patients with chronic hepatitis C (CHC) virus infection and fibrosis. METHODS Twenty-one patients with no or mild fibrosis (METAVIR stage F0, F1) and 23 with advanced fibrosis (F3, F4) were retrospectively identified from a pedigreed database of 1600 CHC patients. All samples were carefully phenotyped and matched for age, gender, race, body mass index, genotype, duration of infection, alcohol use, and viral load. Expression profiling was performed in a blinded fashion using a 2D polyacrylamide gel electrophoresis/LC-MS/MS platform. Partial least squares discriminant analysis and likelihood ratio statistics were used to rank individual differences in protein expression between the 2 groups. RESULTS Seven individual protein spots were identified as either significantly increased (alpha2-macroglobulin, haptoglobin, albumin) or decreased (complement C-4, serum retinol binding protein, apolipoprotein A-1, and two isoforms of apolipoprotein A-IV) with advanced fibrosis. Three individual proteins, haptoglobin, apolipoprotein A-1, and alpha2-macroglobulin, are included in existing non-invasive serum marker panels. CONCLUSION Biomarkers identified through expression profiling may facilitate the development of more accurate marker algorithms to better quantitate hepatic fibrosis and monitor disease progression.

Methylmercury is an environmental contaminant with special selectivity for cerebellar granule cells. The aim of this study was to determine the effect of long-term methylmercury exposure on cell viability and cellular proteome in cultured cerebellar granule cells. Primary cultures of mice cerebellar granule cells were treated with 0-300 nM methylmercury at 2 days in vitro (div) and afterwards the cells were harvested at 12 div. 100 nM methylmercury produced loss of cell viability, reduced intracellular glutamate content and increased lipid peroxidation. Glutamate transport was not modified by methylmercury treatment. Cell death induced by 300 nM methylmercury at 8 div was apoptotic without producing activation of caspase 3. Extracts of total protein were separated by 2D electrophoresis. Around 800 protein spots were visualized by silver staining in SDS-polyacrylamide gels. Gel images were digitized and protein patterns were analysed by image analysis. Several spots were identified through a combination of peptide mass fingerprinting and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). The mitochondrial protein 3-ketoacid-coenzyme A transferase I was decreased up to 39% of controls at concentrations of methylmercury that did not produce cytotoxic effects, whereas the cytoplasmic proteins lactate dehydrogenase chain B and actin did not change. Human & Experimental Toxicology (2007) 26, 263-272.

OBJECTIVE Late diagnosis is the major reason for poor prognosis of pancreatic cancer (PC). Developing new biomarkers of early stage detection is critical. METHODS Proteomic analysis with 2-dimensional gel electrophoresis was used to identify differentially expressed proteins in plasma of PC patients. The 2-dimensional gel electrophoresis plasma protein profiles of 11 PC patients (preoperative and postoperative) were compared with those of 10 patients with chronic pancreatitis (CP) and 11 healthy controls. RESULTS Five proteins were found to be constantly changed. Haptoglobin (Hp) beta chain and leucine-rich alpha2 glycoprotein up-regulated slightly in PC plasma. Pancreatic cancer had a higher frequency of Hp2-2 phenotype but lacked Hp1-1 phenotype. Hemoglobin was increased significantly in plasma samples of PC and CP. Alpha1 antitrypsin gradually increased its expression level in healthy control, PC, and CP. Immunoglobin J chain was elevated in CP plasma samples. Haptoglobin, alpha1 antitrypsin, and leucine-rich alpha2-glycoprotein were all greatly elevated after tumor resection in PC patients. CONCLUSIONS Proteomic analysis can simultaneously detect changes of multiproteins in plasma of PC, but detected proteins are abundant and common plasma proteins and their diagnostic value may be limited.

Toxic oil syndrome (TOS) is a disease that appeared in Spain in 1981 as a consequence of the ingestion of an aniline-adulterated oil illegally marketed as edible. TOS affected more than 20 000 people and produced over 400 deaths in the first 18 months after the outbreak. There is evidence that genetic factors could play a role in the susceptibility of individuals towards the disease. Recently, we suggested that haptoglobin (Hp) polymorphism could also play a role in TOS. To provide a rapid method for high-throughput Hp phenotyping, we developed a two-step MALDI-TOF procedure that allows specific identification of the three common Hp alpha chains. Resolution of the homologous alpha-1s and alpha-1f chains, which have a mass difference of only 0.043 Da, is obtained after guanidination of the protein with O-methylisourea. We applied this procedure to the study of the distribution of the Hp alleles HP(1s), HP(1f), HP(2) in a control versus a TOS-affected population, both originally exposed to the toxic oil. The MALDI-TOF proteotyping method was validated by a parallel analysis of the serum samples by 2-DE. Data obtained from 54 TOS cases and 48 control individuals indicate significant differences in the distribution of Hp phenotypes in the two populations.

Albumin dialysis using the molecular adsorbent recirculating system (MARS) is a new therapeutic approach for liver diseases. To gain insight into the mechanisms involved in albumin dialysis, we analyzed the peptides and proteins absorbed into the MARS strong anion exchange (SAX) cartridges as a result of the treatment of patients with cholestasis and resistant pruritus. Proteins extracted from the SAX MARS cartridges after patient treatment were digested with two enzymes. The resulting peptides were analyzed by multidimensional liquid chromatography coupled to tandem mass spectrometry. We identified over 1,500 peptide sequences corresponding to 144 proteins. In addition to the proteins that are present in control albumin-derived samples, this collection includes 60 proteins that were specific to samples obtained after patient treatment. Five of these proteins (neutrophil defensin 1 [HNP-1], secreted Ly-6/uPAR-related protein 1 [SLURP1], serum amyloid A, fibrinogen alpha chain and pancreatic prohormone) were confirmed to be removed by the dialysis procedure using targeted selected-reaction monitoring MS/MS. Furthermore, capture of HNP-1 and SLURP1 was also validated by Western blot. Interestingly, further analyses of SLURP1 in serum indicated that this protein was 3-fold higher in cholestatic patients than in controls. Proteins captured by MARS share certain structural and biological characteristics, and some of them have important biological functions. Therefore, their removal could be related either to therapeutic or possible adverse effects associated with albumin dialysis.

Major plasma protein families play different roles in blood physiology and hemostasis and in immunodefense. Other proteins in plasma can be involved in signalling as chemical messengers or constitute biological markers of the status of distant tissues. In this respect, the plasma phosphoproteome holds potentially relevant information on the mechanisms modulating these processes through the regulation of protein activity. In this work we describe for the first time a collection of phosphopeptides identified in human plasma using immunoaffinity separation of the seven major serum protein families from other plasma proteins, SCX fractionation, and TiO2 purification prior to LC-MS/MS analysis. One hundred and twenty seven phosphosites in 138 phosphopeptides mapping 70 phosphoproteins were identified with FDR < 1%. A high-confidence collection of phosphosites was obtained using a combined search with the OMSSA, SEQUEST and Phenyx search engines.

Human serum albumin (HSA) solution accounts for 14% of the world market for plasma products. Albumin is indicated for reestablishing and maintaining circulatory volume in situations resulting from traumatic shock, surgery or blood loss. Albumin is also used in extracorporeal liver support devices that perform blood dialysis against this protein. However, the protein composition of therapeutic albumin is only partially known.We performed an exhaustive analysis of albumin composition using a proteomic approach. Low abundance proteins and peptides in these samples were concentrated using a strong anion exchange (SAX) resin. The absorbed material was eluted with a stepwise gradient of ammonium trifluoroacetate and the protein fraction was digested and analyzed by multidimensional liquid chromatography coupled to electrospray tandem mass spectrometry (MDLC-ESIMS/MS) using an LTQ ion trap.A total of 1219 peptides corresponding to 141 proteins different from albumin were identified with a false discovery rate <1%. Near 50% of these proteins have been described previously as forming part of the albuminome. Some of these proteins are proteases (kallikrein) or protease inhibitors (kininogen and SRPK1) or have relevant functions in cell surface adhesion (selectin, cadherins and ICAMs) or in immunity and defense (molecules of the complement system and attractin). Characterization of these proteins and peptides is crucial in order to understand the therapeutic and possible deleterious effects of albumin therapies, in which this solution is infused to treat different pathological conditions.

Current proteomic technology is capable of producing huge amounts of analytical information, which is often difficult to manage in a comprehensive form. Curation, further annotation and public communication of proteomic data require the development of standard data formats and efficient, multimedia database structures. We have implemented a workflow for the annotation of a phosphopeptide database (LymPHOS) that includes tools for MS data filtering and phosphosite assignation, mass spectrum visualization, experimental description and accurate phosphorylation site assignation. Experimental annotations were fitted to current minimum information about a proteomics experiment guidelines. A new guideline for phosphoprotein sample preparation is also proposed. Currently, the database describes 342 phosphorylation sites mapping to more than 200 gene sequences, and it can be accessed through the net (http://www.lymphos.org).

T lymphocytes mediate cellular and humoral defense against foreign bodies or autoantigens. An understanding of T-cell information processing furthers studies of the immunological response. We describe a large-scale phosphorylation analysis of primary T cells using a multidimensional separation strategy, involving preparative SDS-PAGE for prefractionation, in-gel digestion and sequential phosphopeptide enrichment using IMAC and TiO2. A total of 281 phosphorylation sites (197 of high confidence, Ascore > 15), mapping to 204 human gene sequences, were identified by LC-MS(n) analysis in an LTQ linear ion trap. Subsequently, we created the LymPHOS database (http://lymphos.org), which links mass spectrometric peptide information to phosphorylation sites and phosphoprotein sequences.

T lymphocytes mediate cellular and humoral defense against foreign bodies or autoantigens. An understanding of T-cell information processing furthers studies of the immunological response. We describe a large-scale phosphorylation analysis of primary T cells using a multidimensional separation strategy, involving preparative SDS-PAGE for prefractionation, in-gel digestion and sequential phosphopeptide enrichment using IMAC and TiO 2. A total of 281 phosphorylation sites (197 of high confidence, Ascore > 15), mapping to 204 human gene sequences, were identified by LC-MS (n) analysis in an LTQ linear ion trap. Subsequently, we created the LymPHOS database ( http://lymphos.org), which links mass spectrometric peptide information to phosphorylation sites and phosphoprotein sequences.

Pest damage causes important decrease in crop yield every year all over the world, particularly by Lepidoptera. Characterization of the antennal proteins implicated in the reproduction of Lepidoptera will help to develop new methods for pest management and contribute to sustainable agriculture and biodiversity maintenance. We present herein the characterization of some antennal proteins of Sesamia nonagrioides by proteomic techniques such as two-dimensional electrophoresis, MALDI-TOF MS, and electrospray ionization tandem mass spectrometry (ESI-MS/MS). The antennal proteins expressed in both sexes were analyzed and more than 800 spots were detected, finding 16 proteins differentially expressed between males and females. Most of the identified proteins were involved in olfaction. High levels of pheromone binding proteins (PBP1 and PBP2) were found as expected in males, but also in female antennae, although females did not electrophysiologically respond to their own pheromone. General odorant binding proteins (GOBP1 and GOBP2) were preferentially expressed in females but high levels were also detected in males. The expression was remarkably high in both sexes along the complete photoperiod. A sensitive proteomic methodology was developed to identify antennal proteins.

Toxic oil syndrome (TOS) is a disease that appeared in Spain in 1981 as a consequence of the ingestion of an aniline-adulterated oil illegally marketed as edible. TOS affected more than 20 000 people and produced over 400 deaths in the first 18 months after the outbreak. There is evidence that genetic factors could play a role in the susceptibility of individuals towards the disease. Recently, we suggested that haptoglobin (Hp) polymorphism could also play a role in TOS. To provide a rapid method for high-throughput Hp phenotyping, we developed a two-step MALDI-TOF procedure that allows specific identification of the three common Hp alpha chains. Resolution of the homologous alpha-1s and alpha-1f chains, which have a mass difference of only 0.043 Da, is obtained after guanidination of the protein with O-methylisourea. We applied this procedure to the study of the distribution of the Hp alleles HP(1s), HP(1f), HP(2) in a control versus a TOS-affected population, both originally exposed to the toxic oil. The MALDI-TOF proteotyping method was validated by a parallel analysis of the serum samples by 2-DE. Data obtained from 54 TOS cases and 48 control individuals indicate significant differences in the distribution of Hp phenotypes in the two populations.

Photoreceptor chromoproteins undergo light-induced conformational changes that result in a modulation of protein interaction and enzymatic activity. Bacterial phytochromes such as Cph1 from the cyanobacterium Synechocystis PCC 6803 are light-regulated histidine kinases in which the light signal is transferred from the N-terminal chromophore module to the C-terminal kinase module. In this study, purified recombinant Cph1 was subjected to limited proteolysis using trypsin and endoproteinase Glu-C (V8). Cleavage sites of chromopeptide fragments were determined by MALDI-TOF and micro-HPLC on-line with tandem mass spectrometry in an ion trap mass spectrometer. Trypsin produced three major chromopeptides, termed F1 (S56 to R520), F2 (T64 to R472), and F3 (L81 to R472). F1 was produced only in the far-red absorbing form Pfr within 15 min and remained stable up to >1 h; F2 and F3 were obtained in the red-light absorbing form Pr within ca. 5-10 min. When F1 was photoconverted to Pr in the presence of trypsin, this fragment degraded to F2 and F3 within 1-2 min. On size exclusion chromatography, F1 eluted as a dimer in the Pfr and as a monomer in the Pr form, whereas F2 and F3 behaved always as monomers, irrespective of the light conditions. These and other results are discussed in the context of light-dependent subunit interactions, in which amino acids 473-520 within the PHY domain are required for chromophore-module subunit interaction within the homodimer. V8 proteolysis yielded five major chromopeptides, F4 (T17 to N449), F5 (T17 to E335), F6 (T17 to E323), F7 (unknown sequence), and F8 (tentatively L121 to E323). F6 and F8 were formed in the Pr form, whereas F4, F5, and F7 were preferentially formed in the Pfr form. Three amino acids next to specific cleavage sites, R520, R472, and E323, were altered by site-directed mutagenesis. The mutants were analyzed by UV-vis spectroscopy, size exclusion chromatography, and autophosphorylation. Histidine kinase activity was low in R472A, R520P, and R520A; in all mutants, the ratio of phosphorylation intensity between Pr and Pfr was reduced. Thus, light regulation of autophosphorylation is negatively affected in all mutants. In R472P, E323P, and E323D, the phosphorylation intensity of the Pfr form exceeded that of the wild-type control. This result shows that the histidine kinase activity of Cph1 is actively inhibited by photoconversion into Pfr.

Paraquat (PQ) poisoning remains a major public health concern in many countries. Extensive research has focused on finding early diagnostic biomarkers of acute PQ poisoning. In order to investigate the characterization of diagnostic biomarkers in PQ poisoning, we utilized proteomic analysis using serum from rats exposed to PQ, and we identified 8 differentially expressed proteins from over 500 protein spots. The expression of apolipoprotein E (ApoE), preprohaptoglobin (Pphg), a precursor of haptoglobin (Hp), and complement component 3 (C3) proteins was greatly induced by PQ exposure while the expression of fibrinogen γ-chain (FGG) and Ac-158 was dramatically reduced. To further investigate the possibility of ApoE, Pphg and FGG as useful diagnostic biomarkers of PQ poisoning, western blot and qRT-PCR analyses were conducted using cell lines as well as rat and human sera. The expression levels of ApoE, Hp and FGG were significantly altered in the presence of PQ in both rat and human serum suggesting that these proteins may be appropriate candidate molecular biomarkers for the early diagnosis of acute PQ intoxication.

Aspergillus fumigatus is a prime causative agent for various allergic and invasive aspergillosis. There has been a dramatic increase of such cases in last three decades yet the early diagnosis and virulence factor identification remains the challenge. In the present study secretome analysis of proteins isolated from the culture filtrate was done by 2D gel electrophoresis coupled with MS/MS and the immunosecretome analysis was carried out using immunoblotting of 2D transfer blots and probed with the sera of patients, immunized rabbit and mice. The identified proteins were analyzed further for homology with human proteins by BLAST search and for secretory signal by SignalP. A total of 65 protein spots from 2D gel resulted in identification of 24 different proteins along with their isoforms and out of which 15 proteins were identified as immunogenic in human. These findings may be helpful in the identification of virulence factors involved in aspergillosis and also useful as diagnostic markers.

PURPOSE: To investigate the altered expression of proteins in the lens of mice with inherited cataracts. METHODS: Mice with inherited cataracts caused by a spontaneous mutation of the gene gamma S-crystallin (Crygs) were used as the subjects. Lens proteins were extracted and separated by two-dimensional electrophoresis (2-DE). The spots representing differential proteins were first identified by image analysis, and then further analyzed by matrix assisted laser desorption/ionization-time of flight-tandem mass spectrometry (MALDI-TOF-MS/MS). RESULTS: 2-DE were conducted under high (882 mug) and low dosage (190 mug) of sample. Under each condition, the numbers of protein spots found in cataract lenses were similar to those in normal lenses (p>0.05). Seventeen proteins were identified in normal lenses, including alphaA- to alphaB-, betaA1- to betaA4-, betaB1- to betaB3-, gammaA- to gammaF-, and gammaS-crystallin, and bead-filament structure protein (BFSP/filensin). Seven differential ones were consistently identified. In the cataract lenses BFSP and gammaS-crystallin were absent; gammaF-crystallin was downregulated; and betaA1-, betaB1-, betaB2-, and alphaB-crystallin were upregulated. Those abnormally upregulated crystallins, when compared to normal ones, had smaller molecular weight, suggesting possible truncation. CONCLUSIONS: The mutant Crygs gene can lead to changes of BFSP/filensin and other crystallins. The changes to these crystallins, together, may secondarily lead to cataract formation.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a leading cause of significant economic losses in the pig industry worldwide. PRRSV infects preferentially porcine alveolar macrophages (PAMs) and subsequently utilizes the host cell biosynthetic machinery for its own replication. To date, a number of studies have been conducted to investigate compensatory changes of cellular gene expression of PAMs upon PRRSV infection. However, very little information exists about differential cellular protein expression of the natural target cells regulated by each viral protein. This study was therefore designed to examine the dynamics of host protein expression of continuous PAM cells by the PRRSV nucleocapsid (N) protein that is the most abundant and multifunctional viral component. We first established sublines of PAM cells to stably express the PRRSV N protein and assessed alterations in cellular protein productions of N-expressing PAM (PAM-pCD163-N) cells at different time courses by the use of proteomic analysis. A total of 23 protein spots were initially found to be differentially expressed in PAM-pCD163-N cells compared with normal PAM cells by high-resolution two-dimensional gel electrophoresis (2DE). Of these spots, 15 protein spots with statistically significant alteration, including 4 up-regulated and 11 down-regulated protein spots, were picked out for subsequent protein identification by peptide mass fingerprinting after matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS). The altered cellular proteins identified in this study were classified into the functions involved in a variety of cellular processes such as cell division, metabolism, inflammation response, stress response, ubiquitin-proteasome pathway, protein folding and synthesis, and transportation. Notably, heat shock 27kDa protein (HSP27) was found to be up-regulated in PAM-pCD163-N cells. The proteomics data will provide insights into the specific cellular response to the N protein during PRRSV infection.

Two-dimensional electrophoresis is a powerful tool to explore the plant proteome and to unravel changes in protein expression between samples. However, the acquisition of images on which thousands of spots may be resolved has some weak points, as always pointed out by scientists working with gel-free techniques, such as the lack of reproducibility. Nowadays, this inconvenience can be bypassed by the use of a technique known as "difference gel electrophoresis" or DIGE. This technique requires the labelling of proteins by fluorochromes before their separation on 2DE gels. This technique may be applied to a wide array of plant stress studies. Providing accurate quantitative results, differentially abundant spots are usually subjected to tryptic digestion and identified using electrospray ionization, matrix-assisted laser desorption/ionization-time of flight-MS and/or tandem MS.

BACKGROUND The goal of this study was to detect modification in the expression of plasma proteins and/or post-translational modifications of their structure in patients with end stage renal disease. METHODS Serum samples from 19 adult patients treated by maintenance hemodialysis (MHD) were analyzed in comparison to sera from six healthy controls using sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2DE). Spots of interest were identified by mass spectrometry analysis. In addition, the 2DE maps were incubated with a human anti-albumin polyclonal antibody. RESULTS SDS-PAGE gels, 2DE maps and matrix-assisted laser desorption/ionization time of flight analysis indicated over-expression of low-molecular weight proteins (LMWP) in sera from patients. Unexpectedly, another 15 spots with estimated M(r) of 12.5-29 kDa from the 2DE maps of six patients were identified as fragments of albumin. 2D immunoblotting of sera from 12 other patients detected numerous albumin fragments. CONCLUSIONS These results indicate that in addition to increased expression of LMWP, a relevant amount of albumin fragments are detectable in the serum of patients undergoing MHD. Uremia appears to facilitate the fragmentation of albumin and/or the retention of albumin fragments in blood.

OBJECTIVE To investigate the effect of ClpE on the protein expression profiles of Streptococcus pneumoniae. METHODS clpE-deficient Streptococcus pneumoniae strain was constructed by long flanking homology-polymerase chain reaction (LFH-PCR) and identified by PCR and sequencing. The total bacterial proteins were analyzed by two-dimensional gel electrophoresis and imaging analysis, and the differentially expressed protein spots were excised by dot-gel digestion with trypsin. Peptide mass fingerprinting (PMF) was obtained by analysis of the fragment length by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The PMF was analyzed using software to identify the proteins. RESULTS The number of matched protein spots of the two gels was 61%. By sequence database searching, 4 out of the 17 differential protein spots were identified, namely hypoxanthine-guanine, pyrrolidone-carboxylate peptidase1, formate-tetrahydrofolate ligase, and bifunctional protein pyrR. CONCLUSION clpE gene-deficient Streptococcus pneumoniae expresses fewer kinds of proteins at also lower levels than the wild-type bacteria, suggesting that ClpE allows the bacteria to adapt to different host environments by inducing the expression of special proteins.

OBJECTIVE To establish differential protein expression profile specific for serum proteome of cervical carcinoma in Uighur women by protein 2-dimensional liquid phase chromatography. METHODS We collected and prepared sera of cervical carcinoma from Uighur women, and separated and processed data using 2-dimensional liquid phase chromatography system specific for protein (ProteomeLab PF-2D). RESULTS A differential expression profile of serum proteome based on characteristics of protein isoelectric point and hydrophobic features was successfully established. Fifty-six differentially expressed protein spots were found, among which there was an obvious difference in 12 peaks. CONCLUSION Two-dimensional liquid phase chromatography is an effective and feasible method to establish differential expression profile of serum proteome and to offer a new way for the screening of serum protein markers of Uighur women with cervical carcinoma.

Phytochromes are a family of plant photoreceptors that mediate physiological and developmental responses to red and far-red light. According to the affymetrix ATH1 microarray, phytochrome A (phyA) and phytochrome B (phyB) together play a key role in transducing the Rc signals to light-responsive genes. In order to select those red light-responsive genes associated with phyA or phyB, a proteomic approach based on two-dimensional gel electrophoresis (2-DE) was used to compare the protein expression patterns of the phyAphyB double mutant and the wild type of Arabidopsis thaliana (col-4) which grew under constant red light conditions for 7 d. Thirty-two protein spots which exhibited differences in protein abundance were identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. The expression of ten genes corresponding to ten protein spots was analyzed by a semiquantitative reverse transcription-polymerase chain reaction. Two of the ten genes were confirmed by quantitative PCR (Q-PCR). The results showed that phytochromes may exert their function by regulating mRNA or protein expressions. Proteomic analysis may provide a novel pathway for identifying phytochrome-dependent genes.

PURPOSE To analyze the protein expression of human periodontal ligament cells (HPDLCs) under static pressure. METHODS The proteins of two groups of human periodontal ligament cell (one group was interfered by static pressure and one group was not) were analyzed by two-dimensional electrophoresis and mass chromatographic analysis. The silver stained proteins spots were analyzed by Image Master 2D Platinum Software 5.0. There were about 720 and 730 detectable spots on the two 2D-gels separately and nearly 30 spots which were differentially expressed. RESULTS With direct MALDI-TOF mass spectrometry and protein database searching, 2 protein spots out of 5 new appeared spots were identified. Presenilin 2 and catechol O-methyltransferase were expressed only in the group which was interfered by static pressure. CONCLUSIONS The results of mass chromatographic analysis demonstrate that Notch pathway and calcitonin gene-related peptide(CGRP) may be the partners of the channel of biomechanical signal conduction of the periodontal ligament cell.