Isotope-coded Affinity Tag Research Articles

Identification of Replication-competent HSV-1 Cgal+ Strain Signaling Targets in Human Hepatoma Cells by Functional Organelle Proteomics

In the present work, we have attempted a comprehensive analysis of cytosolic and microsomal proteomes to elucidate the signaling pathways impaired in human hepatoma (Huh7) cells upon herpes simplex virus type 1 (HSV-1; Cgal(+)) infection. Using a combination of differential in-gel electrophoresis and nano liquid chromatography/tandem mass spectrometry, 18 spots corresponding to 16 unique deregulated cellular proteins were unambiguously identified, which were involved in the regulation of essential processes such as apoptosis, mRNA processing, cellular structure and integrity, signal transduction, and endoplasmic-reticulum-associated degradation pathway. Based on our proteomic data and additional functional studies target proteins were identified indicating a late activation of apoptotic pathways in Huh7 cells upon HSV-1 Cgal(+) infection. Additionally to changes on RuvB-like 2 and Bif-1, down-regulation of Erlin-2 suggests stimulation of Ca(2+)-dependent apoptosis. Moreover, activation of the mitochondrial apoptotic pathway results from a time-dependent multi-factorial impairment as inferred from the stepwise characterization of constitutive pro- and anti-apoptotic factors. Activation of serine-threonine protein phosphatase 2A (PP2A) was also found in Huh7 cells upon HSV-1 Cgal(+) infection. In addition, PP2A activation paralleled dephosphorylation and inactivation of downstream mitogen-activated protein (MAP) kinase pathway (MEK(1/2), ERK(1/2)) critical to cell survival and activation of proapoptotic Bad by dephosphorylation of Ser-112. Taken together, our results provide novel molecular information that contributes to define in detail the apoptotic mechanisms triggered by HSV-1 Cgal(+) in the host cell and lead to the implication of PP2A in the transduction of cell death signals and cell survival pathway arrest.

Fluorescent isotope‐coded affinity tag 2: Peptide labeling and affinity capture

Fluorescent isotope-coded affinity tag (FCAT) is a novel reagent to label cysteine-containing peptides. The fluorescein group on the tag enables absolute quantification by fluorescence detection, also supporting affinity capture of the labeled peptides. In this paper we report the synthesis of the heavy isotopic form of the FCAT reagent and its use in labeling tryptic peptides. The heavy form of the reagent exhibited the same reactivity and chromatographic behavior that of the light version. Effective labeling of tryptic peptides from alpha-lactalbumin, fetuin, BSA and phosphorylase b was attained by using both the heavy and light FCAT tags. Selective capture of the FCAT-labeled peptides was easily performed by pipette tips containing either anti-FITC antibody or iminodiacetic-acid-coated beads. The differently labeled peptides were separated by RP HPLC and analyzed by MALDI-TOF MS.

Proteomic Characteristics of ex vivo-Enriched Adult Human Bone Marrow Mononuclear Cells in Continuous Perfusion Cultures

A major challenge in developing cell therapies is reliable characterization of the cell product at the molecular level. Fresh autologous and passaged human bone marrow enriched for stem and mesenchymal stromal stem cells have been used to regenerate bone. We report the proteome of an innovative autologous human bone marrow-derived mixed cell product (BMMCP), cultured ex vivo for 12 days, in automated continuous media perfusion system to avoid passaging, and discuss reproducibility of protein composition. Each BMMCP is compared to its originating human adult bone marrow mononuclear cells (BMMNC). With the use of 2-D LC-MS/MS approach, 638 (BMMNC) and 867 (BMMCP) distinct proteins were identified including cell adhesion molecules, extracellular matrix and growth factors. Overlap of protein identifications revealed that 67% of the BMMNC proteome was retained in the BMMCP, and protein expression of selected cell lineages was enhanced. Isotope-coded affinity tags (ICAT) and MS/MS were used to identify and quantify relative changes in the proteome of BMMNC and their related BMMCP, obtained from 3 separate donors. In 3 separate ICAT experiments, 57% of proteome identified was shared between donors. Measurable and definable proteomic characterization of BMMCP will facilitate their use in clinical trials and provide insight into cell functionality needed to support multiple therapeutic indications.

Quantitative Proteomic Analysis of Mitochondria in Aging PS-1 Transgenic Mice

Accumulating evidence suggests mitochondrial alterations are intimately associated with the pathogenesis of Alzheimer's disease (AD). In order to determine if mutations of presenilin-1 (PS-1) affect levels of mitochondrial proteins at different ages we enriched mitochondrial fractions from 3-, 6-, 12-month-old knock-in mice expressing the M146V PS-1 mutation and identified, and quantified proteins using cleavable isotope-coded affinity tag labeling and two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC/MS/MS). Using this approach, 165 non-redundant proteins were identified with 80 of them present in all three age groups. Specifically, at young ages (3 and 6 months), Na(+)/K(+) ATPase and several signal transduction proteins exhibited elevated levels, but dropped dramatically at 12 months. In contrast, components of the oxidative phosporylation pathway (OXPHOS), the mitochondrial permeability transition pore (MPTP), and energy metabolism proteins remained unchanged at 3 months but significantly increased with age. We propose that alterations in calcium homeostasis induced by the PS-1 mutation have a major impact in young animals by inhibiting the function of relevant proteins and inducing compensatory changes. However, in older mice combination of the PS-1 mutation and accumulated oxidative damage results in a functional suppression of OXPHOS and MPTP proteins requiring a compensatory increase in expression levels. In contrast, signal transduction proteins showed decreased levels due to a break down in the compensatory mechanisms. The dysfunction of Na(+)/K(+) ATPase and signal transduction proteins may induce impaired cognition and memory before neurodegeneration occurs.

Towards functional genomics in fish using quantitative proteomics

Microarray and gene expression analysis have been key in our understanding of molecular pathways underlying physiological responses. Arguably, a large number of microarray based studies in fish have examined steroid nuclear receptor signaling (e.g., estrogens, androgens) in the context of both physiology and toxicology. Following close behind the advances in gene expression analysis, novel proteomic tools are available that have been under utilized in fish endocrinology studies. Quantitative proteomic approaches include both gel based (e.g., 2D gel electrophoresis, 2-D Fluorescence Difference Gel Electrophoresis; DIGE) and non-gel based methods that can be separated further into labeling approaches such as stable isotope labeling (SILAC), isotope coded affinity tags (ICAT), and isobaric tagging (iTRAQ ®) and label-free approaches (e.g., spectral counting and absolute quantitation). This review summarizes quantitative proteomic approaches and describes a successful application of iTRAQ ® to study changes in the liver proteome in fathead minnows in response to the androgen, 17β-trenbolone. The challenge remains to integrate molecular datasets in such a manner as to be able to consider temporal effects and complex regulation at the level of the genome and proteome.

S-nitrosylated Cysteins In The Y522S Ca2+ Release Channel RyR1

The Y522S mutation, linked to malignant hyperthermia (MH) and central core diseases in humans, causes a leaky Ca2+ release channel (RyR1), when engineered to mice (RyR1Y522S/wt). The elevated levels of resting Ca2+ in mice harboring the Y522S mutation drive an increased generation of reactive nitrogen species (RNS). S-nitrosylation of the mutant RyR1 increases its temperature sensitivity, resulting in uncontrolled muscle contractions during heat stress, and decreases its sensitivity to Ca2+ inhibition further promoting SR Ca2+ leak, leading to a feedforward cyclic mechanism that continuously increases the temperature sensitivity of RyR1 and RNS production [1].We have used selective isotope coded affinity tag labeling and mass spectroscopy, to identify the cysteines that are endogenously S-nitrosylated in the mutant Ca2+ release channel RyR1 and responsible for its temperature sensitivity.This work was supported by grants from NIH (AR050503 and AR053349) and MDA to SLH[1]. RyR1 S-Nitrosylation Underlies Environmental Heat Stroke and Sudden Death in Y522S RyR1 Knock in Mice, W.J. Durham, P. Aracena-Parks, C. Long, A.E. Rossi, S. A. Goonasekera, S. Boncompagni, D. L. Galvan, C.P. Gilman, M.R. Baker, N. Shirokova, F. Protasi, R. Dirksen, and S.L. Hamilton. Cell, (2008), 133, 53–65.

Apolipoprotein A‐IV, a Putative Satiety/Antiatherogenic Factor, Rises After Gastric Bypass

Roux-en-Y gastric bypass surgery (RYGBP) leads to improvements in satiety and obesity-related comorbidities. The mechanism(s) underlying these improvements are not known but may be revealed in part by discovery proteomics. Therefore, fasting plasma was collected from 12 subjects (mean BMI >45) during RYGBP and during a second procedure approximately 17 months later. Body weight, obesity-related comorbidities, and medication use were decreased after RYGBP. Mass spectrometry-based proteomic analysis was performed on a subset of seven samples using isobaric isotope-coded affinity tags (four plex iTRAQ). Initial proteomic analysis (n = 7) quantified and identified hundreds of plasma proteins. Manual inspection of the data revealed a 2.6 +/- 0.5-fold increase in apolipoprotein A-IV (apo A-IV, gene designation: APOA4), a approximately 46-kDa glycoprotein synthesized mainly in the bypassed small bowel and liver after RYGBP. The change in apo A-IV was significantly greater than other apolipoproteins. Immunoblot analysis of the full longitudinal sample set (n = 12) indicated even higher increases (8.3 +/- 0.2 fold) in apo A-IV. Thus iTRAQ may underestimate the changes in protein concentrations compared to western blotting of apo A-IV. Apo A-IV inhibits gastric emptying and serves as a satiety factor whose synthesis and secretion are increased by the ingestion of dietary fat. It also possesses anti-inflammatory and antiatherogenic properties. Based on these functions, we speculate changes in apo A-IV may contribute to weight loss as well as the improvements in inflammation and cardiovascular disease after RYGBP. In addition, the findings provide evidence validating the use of iTRAQ proteomics in discovery-based studies of post-RYGBP improvements in obesity-related medical comorbidities.

糖尿病におけるプロテオミクス研究の現状と今後の展望

The prevalence of diabetes is rapidly increasing worldwide, thus leading to an increasing risk of diabetic microangiopathy, caused by prolonged hyperglycemia, as well as an increase in atherosclerotic diseases (macroangiopathy), of which diabetes is one of the risk factors. Complex gene-environment interactions make it difficult to investigate the molecular basis of diabetic etiology from clinical samples obtained from diabetic patients with wide-ranging backgrounds. In contrast, risk factors for diabetic complications such as micro- and macroangiopathies are common among patients with a variety of diabetic pathogeneses, thus enabling the proteomic search for biomarkers of diabetic complications from clinical samples feasible. In an attempt to identify diabetic biomarkers, we analyzed sera from more than 100 diabetic patients and approximately 40 control subjects, using cleavable isotope-coded affinity tag, followed by tandem mass spectrometry for protein sequencing and identification. These proteins, which were differentially expressed in the sera from diabetic patients, may be potential biomarkers of various pathological conditions related to diabetes. In another study, we developed a 2-dimensional gel-based method that enabled the analysis of approximately 2,000 protein spots by combining ultrafiltration, immunoaffinity depletion of major urinary proteins, and 2-dimensional difference gel electrophoresis. Using this experimental system, we analyzed urine samples collected from diabetic patients with or without microalbuminuria and healthy controls to search for early diagnostic markers of diabetic nephropathy. We identified 33 unique proteins (24 upregulated and 9 downregulated) that were differentially expressed in diabetic patients with microalbuminuria as compared to those in the healthy controls. Proteomic analyses of clinical samples from diabetic patients, animal models of diabetes, and cultured cells may help to elucidate the molecular mechanisms responsible for the development of various forms of diabetes and to identify diagnostic biomarkers of diabetic complications.

Isotope‐Coded Affinity Tags with Tunable Reactivities for Protein Footprinting

Another foot forward: Isotope-coded affinity tag (ICAT) reagents are versatile probes for footprinting dynamic protein structure. To render ICAT footprinting effective, a series of ICAT reagents with alkylation rates that span five orders of magnitude was designed. With this toolkit, an unprecedented range of Cys residues can be footprinted, including those deeply buried in the protein core and those involved in protein–protein interactions of modest affinity.

Proteomic Profiling in Early Venous Stenosis Formation in a Porcine Model of Hemodialysis Graft

To use proteomic analysis to identify up- and downregulated proteins in early venous stenosis formation in a porcine model of hemodialysis graft failure. Pigs had chronic renal insufficiency created by subtotal renal infarction caused by renal artery embolization. Arteriovenous polytetrafluoroethylene grafts were placed 28 days later and the animals were killed after a further 3 days (n = 4), 7 days (n = 4), or 14 days (n = 4). Proteomic analysis with isotope-coded affinity tags and multidimensional liquid chromatography followed by tandem mass spectrometry was performed on the venous stenosis and control vessels. Expression of proteins was further confirmed by Western blot analysis. The blood urea nitrogen (BUN) and creatinine levels were determined before renal artery embolization and at the time of graft placement. At graft placement, mean BUN and creatinine levels were significantly higher than before embolization (P < .05). Six proteins were identified that were common to all four animals at the same time point. Five proteins (alpha-fetoprotein, fetuin A, macrophage migration inhibitory factor, pyruvate dehydrogenase E1 component, and lactoferrin) were upregulated and one protein (decorin) was downregulated. Expression of macrophage migration inhibitory factor, alpha-fetoprotein, and lactoferrin was further validated with Western blotting. By day 14, lactoferrin and fetuin-A expression were increased significantly in early venous stenosis formation. Significantly increased expression of lactoferrin and fetuin-A were observed in early venous stenosis by day 14. Understanding the role of lactoferrin and fetuin-A in hemodialysis vascular access failure could help in improving outcomes in patients undergoing hemodialysis.

Proteomic Analysis for the Identification of Disease Biomarkers and Therapeutic Targets in Natural Killer Cell Lymphoma.

Natural killer cell lymphoma (NKL) is a highly aggressive form of hematolymphoid malignancy that arises from natural killer cells, a critical component of the innate immune system. Early diagnosis of the tumor is critical however there are no biomarkers which are useful currently for the diagnosis and monitoring of patients with NKLs. We hypothesized that comprehensive analysis of differentially expressed proteins by NKL and normal NK cells would be a rational strategy for the discovery of NKL biomarkers and lead to better understanding of pathogenetic mechanisms of NKL. We used total cell lysates obtained from highly enriched peripheral blood NK cells (CD3-, CD56dim) and an Epstein-Barr virus negative, IL-2 dependent cell line (NK-92MI) for quantitative proteomic analysis. Isotopecoded affinity tags (ICATTM)-labeling followed by liquid chromatography-tandem mass spectrometry analyses (LC-MS/MS) identified 114 differentially expressed proteins in NKL compared to the normal NK cells. Out of these, 80 were upregulated 1.5-fold or greater and 34 were downregulated 1.5-fold or greater in NKL. Proteins within diverse cellular functional categories including cell signaling, transcriptional regulation, DNA metabolism, and immune response were differentially expression. Furthermore, known proteins relevant to the function of NK cells such as perforin, granzyme and defensins were downregulated in the NKL cell line. We selected eight proteins to validate the changes identified by ICAT-LC-MS/MS using Western blot analysis. HSP90, PCNA, alpha-enolase, GSTP1, galectin-1, and PARK7 were upregulated, and lactoferrin and annexin A1 were downregulated by western blot analysis demonstrating high concordance with the results of ICAT-LC-MS/MS analysis. We validated the functional significance of HSP90 as a potential therapeutic target in NKL by investigating the effect of inhibitors of HSP90 (geldanamycin) on the survival of an NKL cell line. Inhibition of HSP90 led to significant decrease in cell viability and apoptotic cell death as confirmed by western blotting demonstration of PARP-1 induction and detection of its cleavage products. This study represents the first global quantitative proteomic cataloguing of proteins expressed by NKL and normal NK cells, and reveals potential candidate proteins that may be useful for the diagnosis and function as therapeutic targets in patients with NKL.

Novel MMP-9 Substrates in Cancer Cells Revealed by a Label-free Quantitative Proteomics Approach

Matrix metalloproteinase-9 (MMP-9) is implicated in tumor metastasis as well as a variety of inflammatory and pathological processes. Although many substrates for MMP-9, including components of the extracellular matrix, soluble mediators such as chemokines, and cell surface molecules have been identified, we undertook a more comprehensive proteomics-based approach to identify new substrates to further understand how MMP-9 might contribute to tumor metastasis. Previous proteomics approaches to identify protease substrates have depended upon differential labeling of each sample. Instead we used a label-free quantitative proteomics approach based on ultraperformance LC-ESI-high/low collision energy MS. Conditioned medium from a human metastatic prostate cancer cell line, PC-3ML, in which MMP-9 had been down-regulated by RNA interference was compared with that from the parental cells. From more than 200 proteins identified, 69 showed significant alteration in levels after depletion of the protease (>+/-2-fold), suggesting that they might be candidate substrates. Levels of six of these (amyloid-beta precursor protein, collagen VI, leukemia inhibitory factor, neuropilin-1, prostate cancer cell-derived growth factor (PCDGF), and protease nexin-1 (PN-1)) were tested in the conditioned media by immunoblotting. There was a strong correlation between results by ultraperformance LC-ESI-high/low collision energy MS and by immunoblotting giving credence to the label-free approach. Further information about MMP-9 cleavage was obtained by comparison of the peptide coverage of collagen VI in the presence and absence of MMP-9 showing increased sensitivity of the C- and N-terminal globular regions over the helical regions. Susceptibility of PN-1 and leukemia inhibitory factor to MMP-9 degradation was confirmed by in vitro incubation of the recombinant proteins with recombinant MMP-9. The MMP-9 cleavage sites in PN-1 were sequenced. This study provides a new label-free method for degradomics cell-based screening leading to the identification of a series of proteins whose levels are affected by MMP-9, some of which are clearly direct substrates for MMP-9 and become candidates for involvement in metastasis.

New technologies for diagnosing pediatric tumors

BACKGROUND: The completion of Human Genome Project (HGP) has paved the way for novel, more detailed and accurate molecular diagnostic classification of cancer. With the information from the HGP, cancers can be categorized not only on the morphology or limited immunohistological markers, but according to their "molecular fingerprints" such as gene expression profiles. Technologies detecting these signatures have been developed to simultaneously measure multiple genes or proteins in one assay with high sensitivity and specificity. OBJECTIVE: To evaluate potential innovative novel methods of diagnosis and prognosis in pediatric cancers. METHODS: We selected a variety of promising new diagnostic technologies utilizing molecular signatures which harness the results from HGP including DNA microarray, bead-based detection system, multiplexed RT-PCR, MesoScale Discovery (MSD), and isotope-coded affinity tag (ICAT), as well as their applications in biomarker discovery for pediatric tumors. Label-free detection technologies and the obstacles for taking these new diagnostic technologies from the bench to the bedside are also discussed. CONCLUSION: The use of molecular signatures is gaining acceptance in clinical practice. However, technical challenges need to be addressed before incorporating these new technologies into current diagnostic and prognostic schema.

Identification of Thioredoxin Disulfide Targets Using a Quantitative Proteomics Approach Based on Isotope-Coded Affinity Tags

Thioredoxin (Trx) is a ubiquitous protein disulfide reductase involved in a wide range of cellular redox processes. A large number of putative target proteins have been identified using proteomics approaches, but insight into target specificity at the molecular level is lacking since the reactivity of Trx toward individual disulfides has not been quantified. Here, a novel proteomics procedure is described for quantification of Trx-mediated target disulfide reduction based on thiol-specific differential labeling with the iodoacetamide-based isotope-coded affinity tag (ICAT) reagents. Briefly, protein extract of embryos from germinated barley seeds was treated +/- Trx, and thiols released from target protein disulfides were irreversibly blocked with iodoacetamide. The remaining cysteine residues in the Trx-treated and the control (-Trx) samples were then chemically reduced and labeled with the "light" (12C) and "heavy" (13C) ICAT reagent, respectively. The extent of Trx-mediated reduction was thus quantified for individual cysteine residues based on ratios of tryptic peptides labeled with the two ICAT reagents as measured by liquid chromatography coupled with mass spectrometry (LC-MS). A threshold for significant target reduction was set and disulfide targets were identified in 104 among a total of 199 identified ICAT-labeled peptides. Trx-reduced disulfides were found in several previously identified target proteins, for example, peroxiredoxin and cyclophilin, as well as from a wide range of new targets including several ribosomal proteins that point to a link between Trx h and translation. The catalytic cysteine in dehydroascorbate reductase constituted the most extensively reduced target suggesting that Trx h has an important role in the ascorbate-glutathione cycle.

Fluorescent isotope-coded affinity tag (FCAT) I: Design and synthesis

A novel class of isotope-coded affinity tag is proposed possessing a fluorescent feature, referred to as fluorescent isotope-coded affinity tag (FCAT), to provide a new tool for quantitative proteomics. The label is designed to bind cysteine containing proteins or peptides. The FCAT reagent comprises four functional elements: a specific chemical reactivity group toward sulfhydryl groups; a linker that can incorporate the stable isotopes; a hydroxymethylbenzoic residue (base labile group) to cleave off a large part of the label before MS analysis; and a fluorescent tag for absolute quantification. The fluorescent part of the tag is also planned to be utilized to isolate the FCAT-labeled peptides via antibody based pull-down method. In this paper, we report on the solid phase organic synthesis of the light isotope containing FCAT molecule. The new labeling reagent showed good reactivity with model cysteine containing peptides. The fluorophore group was also effectively cleaved off from the labeled products to accommodate easier MS based analysis.

D-Dopachrome tautomerase is a candidate for key proteins to protect the rat liver damaged by carbon tetrachloride

Carbon tetrachloride (CCl 4) is known to induce liver damage. Animal experiments with CCl 4 injections have revealed many findings, especially mechanisms of liver damage and liver regeneration. Recently, proteomic approaches have been introduced in various studies to evaluate the quantitative and qualitative changes in the comprehensive proteome level. The aim of this research is to elucidate the key protein for liver damage, liver protection and liver regeneration by using proteomic techniques. 50 % (v/v) CCl 4 in corn oil was administered intraperitoneally to adult male rats at a dose of 4 ml/kg body weight. Approximately 24 h after the injection, the liver was removed and extracted proteins were analyzed with cleavable isotope coded affinity tag (cICAT) reagents, two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). A twelvefold increase in d-dopachrome tautomerase (DDT) was indicated. This enzyme has been reported to be involved in the biosynthesis of melanin, an antioxidant. According to the histological analysis, melanin levels were increased in un-damaged hepatocytes of CCl 4-treated rats. These results suggest that the increase in DDT is a response to liver damage, accelerates melanin biosynthesis and protects the liver from oxidative stress induced by CCl 4.

Capn4 overexpression underlies tumor invasion and metastasis after liver transplantation for hepatocellular carcinoma #

Liver transplantation (LT) is one of the best therapeutic options for nonresectable hepatocellular carcinoma (HCC). Unfortunately, some HCC patients succumb to the disease after LT, which reduces long- and medium-term survival. To identify the proteins associated with HCC invasion and metastasis, HCC patients undergoing LT with complete follow-up data were included in this study and were categorized into recurrence and nonrecurrence groups. We extracted the total protein from the acquired homogeneous tumor cells and applied a cleavable isotope-coded affinity tag technology to quantitate relative changes in protein levels between the two groups. We identified a total of 149 proteins with two-dimensional liquid chromatography coupled with tandem mass spectrometry, including 52 differentially expressed proteins by at least two-fold. Among them, calpain small subunit 1 (Capn4), a protein with relevant interactions with many migration-invasion-related proteins, has attracted more attention. First, Capn4 overexpression in the recurrence group was confirmed via real-time polymerase chain reaction and western blotting in another cohort of 40 HCC patients undergoing LT. Second, Capn4 was associated with enhanced invasiveness in vitro. The small interfering RNA-mediated knockdown expression of Capn4 in HCC cell lines significantly inhibited its mobile and invasive ability. Tissue microarray in a further 192 cases revealed that Capn4 significantly correlated with invasive phenotype of HCC, and univariate and multivariate analyses indicated that Capn4 is an independent prognostic factor for recurrence and survival of HCC patients. Our study revealed that Capn4 overexpression underlies invasion and metastasis after LT for HCC and might be a candidate biomarker for future diagnosis and a target for therapy.

Automated Online Sequential Isotope Labeling for Protein Quantitation Applied to Proteasome Tissue-specific Diversity

Quantitation of protein abundance is a vital component in the proteomic analysis of biological systems, which can be achieved by differential stable isotopic labeling. To analyze tissue-derived samples, the isotopic labeling can be performed using chemical labeling of the peptides post-digestion. Standard chemical labeling procedures often require many manual sample handling steps, reducing the accuracy of measurements. Here, we describe a fully automated, online (in nanoLC columns), labeling procedure, which allows protein quantitation using differential isotopic dimethyl labeling of peptide N termini and lysine residues. We show that the method allows reliable quantitation over a wide dynamic range and can be used to quantify differential protein abundances in lysates and, more targeted, differences in composition between purified protein complexes. We apply the method to determine the differences in composition between bovine liver and spleen 20 S core proteasome complexes. We find that although all catalytically active immunoproteasome subunits were up-regulated in spleen (compared with liver), only one of the normal catalytic subunits was down-regulated, suggesting that the tissue-specific immunoproteasome assembly is more diverse than previously assumed.

Prevention of Amino Acid Conversion in SILAC Experiments with Embryonic Stem Cells

Recent studies using stable isotope labeling with amino acids in culture (SILAC) in quantitative proteomics have made mention of the problematic conversion of isotope-coded arginine to proline in cells. The resulting converted proline peptide divides the heavy peptide ion signal causing inaccuracy when compared with the light peptide ion signal. This is of particular concern as it can effect up to half of all peptides in a proteomic experiment. Strategies to both compensate for and limit the inadvertent conversion have been demonstrated, but none have been shown to prevent it. Additionally, these methods combined with SILAC labeling in general have proven problematic in their large scale application to sensitive cell types including embryonic stem cells (ESCs) from the mouse and human. Here, we show that by providing as little as 200 mg/liter L-proline in SILAC media, the conversion of arginine to proline can be rendered completely undetectable. At the same time, there was no compromise in labeling with isotope-coded arginine, indicating there is no observable back conversion from the proline supplement. As a result, when supplemented with proline, correct interpretation of "light" and "heavy" peptide ratios could be achieved even in the worst cases of conversion. By extending these principles to ESC culture protocols and reagents we were able to routinely SILAC label both mouse and human ESCs in the absence of feeder cells and without compromising the pluripotent phenotype. This study provides the simplest protocol to prevent proline artifacts in SILAC labeling experiments with arginine. Moreover, it presents a robust, feeder cell-free, protocol for performing SILAC experiments on ESCs from both the mouse and the human.

Quantitative Analysis of Redox-Sensitive Proteome with DIGE and ICAT

Oxidative modifications of protein thiols are important mechanisms for regulating protein functions. The present study aimed to compare the relative effectiveness of two thiol-specific quantitative proteomic techniques, difference gel electrophoresis (DIGE) and isotope coded affinity tag (ICAT), for the discovery of redox-sensitive proteins in heart tissues. We found that these two methods were largely complementary; each could be used to reveal a set of unique redox-sensitive proteins. Some of these proteins are low-abundant signaling proteins and membrane proteins. From DIGE analysis, we found that both NF-kappaB-repressing protein and epoxide hydrolase were sensitive to H 2O 2 oxidation. In ICAT analysis, we found that specific cysteines within sacroplasmic endoplamic reticulum calcium ATPase 2 and voltage-dependent anion-selective channel protein 1 were sensitive to H 2O 2 oxidation. From these analyses, we conclude that both methods should be employed for proteome-wide studies, to maximize the possibility of identifying proteins containing redox-sensitive cysteinyl thiols in complex biological systems.