Displaying publications 21 - 40 of 87 in total

Abstract:
Sort:
  1. Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp
    Al-Obaidi JR, Saidi NB, Usuldin SR, Hussin SN, Yusoff NM, Idris AS
    Protein J, 2016 Apr;35(2):100-6.
    PMID: 27016942 DOI: 10.1007/s10930-016-9656-z
    Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant-fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp.
    Matched MeSH terms: Proteomics/methods*
  2. Probing the endogenous peptidomes of cancer for biomarkers: A new endeavor
    Lee PY, Low TY, Jamal R
    Adv Clin Chem, 2018 12 27;88:67-89.
    PMID: 30612607 DOI: 10.1016/bs.acc.2018.10.004
    The life span of cancer patients can be prolonged with appropriate therapies if detected early. Mass screening for early detection of cancer, however, requires sensitive and specific biomarkers obtainable from body fluids such as blood or urine. To date, most biomarker discovery programs focus on the proteome rather than the endogenous peptidome. It has been long-established that tumor cells and stromal cells produce tumor resident proteases (TRPs) to remodel the surrounding tumor microenvironment in support of tumor progression. In fact, proteolytic products of TRPs have been shown to correlate with malignant behavior. Being of low molecular weight, these unique peptides can pass through the endothelial barrier of the vasculature into the bloodstream. As such, the cancer peptidome has increasingly become a focus for biomarker discovery. In this review, we discuss on the various aspects of the peptidome in cancer biomarker research.
    Matched MeSH terms: Proteomics/methods
  3. Development of a rapid and improved two-dimensional electrophoresis method for the separation of protein lysate
    Kwan SH, Ismail MN
    Biomed Chromatogr, 2019 Dec;33(12):e4686.
    PMID: 31452214 DOI: 10.1002/bmc.4686
    Researchers frequently use two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) prior to mass spectrometric analysis in a proteomics approach. The i2D-PAGE method, which 'inverts' the dimension of protein separation of the conventional 2D-PAGE, is presented in this publication. Protein lysate of Channa striata, a freshwater snakehead fish, was separated based on its molecular weight in the first dimension and its isoelectric point in the second dimension. The first-dimension separation was conducted on a gel-free separation device, and the protein mixture was fractionated into 12 fractions in chronological order of increasing molecular weight. The second-dimension separation featured isoelectric focusing, which further separated the proteins within the same fraction according to their respective isoelectric point. Advantages of i2D-PAGE include better visualisation of the isolated protein, easy identification on protein isoforms, shorter running time, customisability and reproducibility. Erythropoietin standard was applied to i2D-PAGE to show its effectiveness for separating protein isoforms. Various staining methods such as Coomassie blue staining and silver staining are also applicable to i2D-PAGE. Overall, the i2D-PAGE separation method effectively separates protein lysate and is suitable for application in proteomics research.
    Matched MeSH terms: Proteomics/methods
  4. Fulltext N-glycan MALDI Imaging Mass Spectrometry on Formalin-Fixed Paraffin-Embedded Tissue Enables the Delineation of Ovarian Cancer Tissues
    Everest-Dass AV, Briggs MT, Kaur G, Oehler MK, Hoffmann P, Packer NH
    Mol Cell Proteomics, 2016 09;15(9):3003-16.
    PMID: 27412689 DOI: 10.1074/mcp.M116.059816
    Ovarian cancer is a fatal gynaecological malignancy in adult women with a five-year overall survival rate of only 30%. Glycomic and glycoproteomic profiling studies have reported extensive protein glycosylation pattern alterations in ovarian cancer. Therefore, spatio-temporal investigation of these glycosylation changes may unearth tissue-specific changes that occur in the development and progression of ovarian cancer. A novel method for investigating tissue-specific N-linked glycans is using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) on formalin-fixed paraffin-embedded (FFPE) tissue sections that can spatially profile N-glycan compositions released from proteins in tissue-specific regions. In this study, tissue regions of interest (e.g. tumor, stroma, adipose tissue and necrotic areas) were isolated from FFPE tissue sections of advanced serous ovarian cancers (n = 3). PGC-LC-ESI-MS/MS and MALDI-MSI were used as complementary techniques to firstly generate structural information on the tissue-specific glycans in order to then obtain high resolution images of the glycan structure distribution in ovarian cancer tissue. The N-linked glycan repertoires carried by the proteins in these tissue regions were structurally characterized for the first time in FFPE ovarian cancer tissue regions, using enzymatic peptide-N-glycosidase F (PNGase F) release of N-glycans. The released glycans were analyzed by porous graphitized carbon liquid chromatography (PGC-LC) and collision induced electrospray negative mode MS fragmentation analysis. The N-glycan profiles identified by this analysis were then used to determine the location and distribution of each N-glycan on FFPE ovarian cancer sections that were treated with PNGase F using high resolution MALDI-MSI. A tissue-specific distribution of N-glycan structures identified particular regions of the ovarian cancer sections. For example, high mannose glycans were predominantly expressed in the tumor tissue region whereas complex/hybrid N-glycans were significantly abundant in the intervening stroma. Therefore, tumor and non-tumor tissue regions were clearly demarcated solely on their N-glycan structure distributions.
    Matched MeSH terms: Proteomics/methods
  5. Fulltext Chemometrics of differentially expressed proteins from colorectal cancer patients
    Yeoh LC, Dharmaraj S, Gooi BH, Singh M, Gam LH
    World J Gastroenterol, 2011 Apr 28;17(16):2096-103.
    PMID: 21547128 DOI: 10.3748/wjg.v17.i16.2096
    To evaluate the usefulness of differentially expressed proteins from colorectal cancer (CRC) tissues for differentiating cancer and normal tissues.
    Matched MeSH terms: Proteomics/methods*
  6. Proteomic investigation of Sri Lankan hump-nosed pit viper (Hypnale hypnale) venom
    Tan CH, Tan NH, Sim SM, Fung SY, Gnanathasan CA
    Toxicon, 2015 Jan;93:164-70.
    PMID: 25451538 DOI: 10.1016/j.toxicon.2014.11.231
    The hump-nosed pit viper, Hypanle hypnale, contributes to snakebite mortality and morbidity in Sri Lanka. Studies showed that the venom is hemotoxic and nephrotoxic, with some biochemical and antigenic properties similar to the venom of Calloselasma rhodostoma (Malayan pit viper). To further characterize the complexity composition of the venom, we investigated the proteome of a pooled venom sample from >10 Sri Lankan H. hypnale with reverse-phase high performance liquid chromatography (rp-HPLC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and peptide sequencing (tandem mass-spectrometry and/or N-terminal sequencing). The findings ascertained that two phospholipase A2 subtypes (E6-PLA2, W6-PLA2) dominate the toxin composition by 40.1%, followed by snake venom metalloproteases (36.9%), l-amino acid oxidase (11.9%), C-type lectins (5.5%), serine proteases (3.3%) and others (2.3%). The presence of the major toxins correlates with the venom's major pathogenic effects, indicating these to be the principal target toxins for antivenom neutralization. This study supports the previous finding of PLA2 dominance in the venom but diverges from the view that H. hypnale venom has low expression of large enzymatic toxins. The knowledge of the composition and abundance of toxins is essential to elucidate the pathophysiology of H. hypnale envenomation and to optimize antivenom formulation in the future.
    Matched MeSH terms: Proteomics/methods*
  7. Proteomics in commercial crops: An overview
    Tan BC, Lim YS, Lau SE
    J Proteomics, 2017 10 03;169:176-188.
    PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018
    Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

    SIGNIFICANCE: Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

    Matched MeSH terms: Proteomics/methods*
  8. Unrestrictive identification of post-translational modifications in Hevea brasiliensis latex
    Habib MAH, Gan CY, Abdul Latiff A, Ismail MN
    Biochem. Cell Biol., 2018 12;96(6):818-824.
    PMID: 30058361 DOI: 10.1139/bcb-2018-0020
    The natural rubber latex extracted from the bark of Hevea brasiliensis plays various important roles in modern society. Post-translational modifications (PTMs) of the latex proteins are important for the stability and functionality of the proteins. In this study, latex proteins were acquired from the C-serum, lutoids, and rubber particle layers of latex without using prior enrichment steps; they were fragmented using collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron-transfer dissociation (ETD) activation methods. PEAKS 7 were used to search for unspecified PTMs, followed by analysis through PTM prediction tools to crosscheck both results. There were 73 peptides in 47 proteins from H. brasiliensis protein sequences derived from UniProtKB were identified and predicted to be post-translationally modified. The peptides with PTMs identified include phosphorylation, lysine acetylation, N-terminal acetylation, hydroxylation, and ubiquitination. Most of the PTMs discovered have yet to be reported in UniProt, which would provide great assistance in the research of the functional properties of H. brasiliensis latex proteins, as well as being useful biomarkers. The data are available via the MassIVE repository with identifier MSV000082419.
    Matched MeSH terms: Proteomics/methods
  9. An effective placental cotyledons proteins extraction method for 2D gel electrophoresis
    Tan NJ, Daim LD, Jamil AA, Mohtarrudin N, Thilakavathy K
    Electrophoresis, 2017 03;38(5):633-644.
    PMID: 27992069 DOI: 10.1002/elps.201600377
    Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen.
    Matched MeSH terms: Proteomics/methods
  10. Deciphering key proteins of oil palm (Elaeis guineensis Jacq.) fruit mesocarp development by proteomics and chemometrics
    Hassan H, Amiruddin MD, Weckwerth W, Ramli US
    Electrophoresis, 2019 01;40(2):254-265.
    PMID: 30370930 DOI: 10.1002/elps.201800232
    Palm oil is an edible vegetable oil derived from lipid-rich fleshy mesocarp tissue of oil palm (Elaeis guineensis Jacq.) fruit and is of global economic and nutritional relevance. While the understanding of oil biosynthesis in plants is improving, the fundamentals of oil biosynthesis in oil palm still require further investigations. To gain insight into the systemic mechanisms that govern oil synthesis during oil palm fruit ripening, the proteomics approach combining gel-based electrophoresis and mass spectrometry was used to profile protein changes and classify the patterns of protein accumulation during these complex physiological processes. Protein profiles from different stages of fruit ripening at 10, 12, 14, 15, 16, 18 and 20 weeks after anthesis (WAA) were analysed by two-dimensional gel electrophoresis (2DE). The proteome data were then visualised using a multivariate statistical analysis of principal component analysis (PCA) to get an overview of the proteome changes during the development of oil palm mesocarp. A total of 68 differentially expressed protein spots were successfully identified by matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF/TOF) and functionally classified using ontology analysis. Proteins related to lipid production, energy, secondary metabolites and amino acid metabolism are the most significantly changed proteins during fruit development representing potential candidates for oil yield improvement endeavors. Data are available via ProteomeXchange with identifier PXD009579. This study provides important proteome information for protein regulation during oil palm fruit ripening and oil synthesis.
    Matched MeSH terms: Proteomics/methods*
  11. The evolution of two-dimensional gel electrophoresis - from proteomics to emerging alternative applications
    Lee PY, Saraygord-Afshari N, Low TY
    J Chromatogr A, 2020 Mar 29;1615:460763.
    PMID: 31836310 DOI: 10.1016/j.chroma.2019.460763
    Two-dimensional gel electrophoresis (2-DE) is a technique that has been widely applied in a variety of proteomics studies. It is capable of resolving complex protein mixtures into individual protein spots based on their isoelectric point and molecular weight, enabling large-scale analysis of protein expression patterns for deciphering their changes in different biological conditions. 2-DE is a powerful tool that empowers researchers to perform differential qualitative and quantitative proteome analysis and is particularly advantageous for characterizing protein isoforms and post-translationally modified proteins. Despite its popularity as the workhorse for proteomics in the past few decades, it has been gradually displaced by the more sophisticated and high-performance mass spectrometry-based methods. However, there are several variations of the 2-DE technique that have emerged as promising approaches that shine new light on specific niches that 2-DE could still contribute. In this review, we first provide an overview of the applications of 2-DE, its merits and pitfalls in the current proteomic research arena, followed by a discussion on several alternative approaches for potential future applications.
    Matched MeSH terms: Proteomics/methods*
  12. Fulltext Development of high-performance two-dimensional gel electrophoresis for human hair shaft proteome
    Wong SY, Hashim OH, Hayashi N
    PLoS One, 2019;14(3):e0213947.
    PMID: 30889197 DOI: 10.1371/journal.pone.0213947
    The primary components of human hair shaft-keratin and keratin-associated proteins (KAPs), together with their cross-linked networks-are the underlying reason for its rigid structure. It is therefore requisite to overcome the obstacle of hair insolubility and establish a reliable protocol for the proteome analysis of this accessible specimen. The present study employed an alkaline-based method for the efficient isolation of hair proteins and subsequently examined them using gel-based proteomics. The introduction of two proteomic protocols, namely the conventional and modified protocol, have resulted in the detection of more than 400 protein spots on the two-dimensional gel electrophoresis (2DE). When compared, the modified protocol is deemed to improve overall reproducibility, whilst offering a quick overview of the total protein distribution of hair. The development of this high-performance protocol is hoped to provide a new approach for hair analysis, which could possibly lead to the discovery of biomarkers for hair in health and diseases in the future.
    Matched MeSH terms: Proteomics/methods*
  13. Comparative venom proteomics of banded krait (Bungarus fasciatus) from five geographical locales: Correlation of venom lethality, immunoreactivity and antivenom neutralization
    Hia YL, Tan KY, Tan CH
    Acta Trop, 2020 Jul;207:105460.
    PMID: 32278639 DOI: 10.1016/j.actatropica.2020.105460
    The banded krait, Bungarus fasciatus is a medically important venomous snake in Asia. The wide distribution of this species in Southeast Asia and southern China indicates potential geographical variation of the venom which may impact the clinical management of snakebite envenomation. This study investigated the intraspecific venom variation of B. fasciatus from five geographical locales through a venom decomplexing proteomic approach, followed by toxinological and immunological studies. The venom proteomes composed of a total of 9 toxin families, comprising 22 to 31 proteoforms at varying abundances. The predominant proteins were phospholipase A2 (including beta-bungarotoxin), Kunitz-type serine protease inhibitor (KSPI) and three-finger toxins (3FTx), which are toxins that cause neurotoxicity and lethality. The venom lethality varied with geographical origins of the snake, with intravenous median lethal doses (LD50) ranging from 0.45-2.55 µg/g in mice. The Thai Bungarus fasciatus monovalent antivenom (BFMAV) demonstrated a dose-dependent increasing immunological binding activity toward all venoms; however, its in vivo neutralization efficacy varied vastly with normalized potency values ranging from 3 to 28 mg/g, presumably due to the compositional differences of dominant proteins in the different venoms. The findings support that antivenom use should be optimized in different geographical areas. The development of a pan-regional antivenom may be a more sustainable solution for the treatment of snakebite envenomation.
    Matched MeSH terms: Proteomics/methods*
  14. Proteomics Identification of Potential Candidates Involved in Cell Proliferation for Early Stage of Brain Regeneration in the Adult Zebrafish
    Lim FT, Ogawa S, Smith AI, Parhar IS
    Zebrafish, 2017 Feb;14(1):10-22.
    PMID: 27797681 DOI: 10.1089/zeb.2016.1319
    The central nervous system (CNS) of the non-mammalian vertebrates has better neuroregenerative capability as compared with the mammalian CNS. Regeneration of habenula was observed 40 days after damage in zebrafish. During the early stage of regeneration, we found a significant increase of apoptotic cells on day-1 post-damage and of proliferative cells on day-3 post-damage. To identify the molecular factor(s) involved in the early stages of neuroregeneration, differentially expressed proteins during sham, 20- and 40-h post-habenula damage were investigated by proteomic approach by using two-dimensional differential gel electrophoresis (2D-DIGE) coupled with Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight (MALDI-ToF) and tandem mass spectrometry. Protein profiles revealed 17 differentially (>1.5-fold) expressed proteins: 10 upregulated, 4 downregulated, 2 proteins were found to be downregulated at the early stage but upregulated at a later stage, and 1 protein was found to be upregulated at 2 different time points. All proteins identified can be summarized under few molecular processes involved in the early stages of neuroregeneration in zebrafish CNS: apoptosis regulation (Wnt inhibitory factor 1 [WIF1]), neuroprotection (metallothionein), cell proliferation (Spred2, ependymin, Lhx1, and Wnts), differentiation (Spred2, Lhx9, and Wnts), and morphogenesis (cytoplasmic actins and draculin). These protein profiling results suggest that drastic molecular changes occur in the neuroregenerative process during this period, which includes cell proliferation, differentiation, and protection.
    Matched MeSH terms: Proteomics/methods*
  15. Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine
    Ang MY, Low TY, Lee PY, Wan Mohamad Nazarie WF, Guryev V, Jamal R
    Clin Chim Acta, 2019 Nov;498:38-46.
    PMID: 31421119 DOI: 10.1016/j.cca.2019.08.010
    One of the best-established area within multi-omics is proteogenomics, whereby the underpinning technologies are next-generation sequencing (NGS) and mass spectrometry (MS). Proteogenomics has contributed significantly to genome (re)-annotation, whereby novel coding sequences (CDS) are identified and confirmed. By incorporating in-silico translated genome variants in protein database, single amino acid variants (SAAV) and splice proteoforms can be identified and quantified at peptide level. The application of proteogenomics in cancer research potentially enables the identification of patient-specific proteoforms, as well as the association of the efficacy or resistance of cancer therapy to different mutations. Here, we discuss how NGS/TGS data are analyzed and incorporated into the proteogenomic framework. These sequence data mainly originate from whole genome sequencing (WGS), whole exome sequencing (WES) and RNA-Seq. We explain two major strategies for sequence analysis i.e., de novo assembly and reads mapping, followed by construction of customized protein databases using such data. Besides, we also elaborate on the procedures of spectrum to peptide sequence matching in proteogenomics, and the relationship between database size on the false discovery rate (FDR). Finally, we discuss the latest development in proteogenomics-assisted precision oncology and also challenges and opportunities in proteogenomics research.
    Matched MeSH terms: Proteomics/methods
  16. Fulltext The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids
    Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA, Kovalchuk SI, Azarkin IV, et al.
    Mol Cell Proteomics, 2016 Jul;15(7):2366-78.
    PMID: 27143409 DOI: 10.1074/mcp.M115.056036
    Acute inflammatory demyelinating polyneuropathy (AIDP) - the main form of Guillain-Barre syndrome-is a rare and severe disorder of the peripheral nervous system with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis and control patients. A total protein concentration increase was shown to be because of even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Because of the studies of the acute motor axonal form, Guillain-Barre syndrome as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed cell adhesion proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however, AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, whereas innate immunity cytokines were up-regulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary peripheral nervous system damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, whereas the autoantibody production might be an optional complementary secondary process.
    Matched MeSH terms: Proteomics/methods*
  17. Use of tryptic peptide MALDI mass spectrometry imaging to identify the spatial proteomic landscape of colorectal cancer liver metastases
    Li CMY, Briggs MT, Lee YR, Tin T, Young C, Pierides J, et al.
    Clin Exp Med, 2024 Mar 16;24(1):53.
    PMID: 38492056 DOI: 10.1007/s10238-024-01311-5
    Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. CRC liver metastases (CRLM) are often resistant to conventional treatments, with high rates of recurrence. Therefore, it is crucial to identify biomarkers for CRLM patients that predict cancer progression. This study utilised matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to spatially map the CRLM tumour proteome. CRLM tissue microarrays (TMAs) of 84 patients were analysed using tryptic peptide MALDI-MSI to spatially monitor peptide abundances across CRLM tissues. Abundance of peptides was compared between tumour vs stroma, male vs female and across three groups of patients based on overall survival (0-3 years, 4-6 years, and 7+ years). Peptides were then characterised and matched using LC-MS/MS. A total of 471 potential peptides were identified by MALDI-MSI. Our results show that two unidentified m/z values (1589.876 and 1092.727) had significantly higher intensities in tumours compared to stroma. Ten m/z values were identified to have correlation with biological sex. Survival analysis identified three peptides (Histone H4, Haemoglobin subunit alpha, and Inosine-5'-monophosphate dehydrogenase 2) and two unidentified m/z values (1305.840 and 1661.060) that were significantly higher in patients with shorter survival (0-3 years relative to 4-6 years and 7+ years). This is the first study using MALDI-MSI, combined with LC-MS/MS, on a large cohort of CRLM patients to identify the spatial proteome in this malignancy. Further, we identify several protein candidates that may be suitable for drug targeting or for future prognostic biomarker development.
    Matched MeSH terms: Proteomics/methods
  18. Fulltext The differential expression of aqueous soluble proteins in breast normal and cancerous tissues in relation to stage and grade of patients
    Liang S, Singh M, Gam LH
    J Biomed Biotechnol, 2010;2010:516469.
    PMID: 21197096 DOI: 10.1155/2010/516469
    Breast cancer is a leading cause of female deaths worldwide. In Malaysia, it is the most common form of female cancer while Infiltrating ductal carcinoma (IDC) is the most common form of breast cancer. A proteomic approach was used to identify changes in the protein profile of breast cancerous and normal tissues. The patients were divided into different cohorts according to tumour stage and grade. We identified twenty-four differentially expressed hydrophilic proteins. A few proteins were found significantly related to various stages and grades of IDC, amongst which were SEC13-like 1 (isoform b), calreticulin, 14-3-3 protein zeta, and 14-3-3 protein eta. In this study, we found that by defining the expression of the proteins according to stages and grades of IDC, a significant relationship between the expression of the proteins with the stage or grade of IDC can be established, which increases the usefulness of these proteins as biomarkers for IDC.
    Matched MeSH terms: Proteomics/methods*
  19. Fulltext Genome-based proteomic analysis of Lignosus rhinocerotis (Cooke) Ryvarden sclerotium
    Yap HY, Fung SY, Ng ST, Tan CS, Tan NH
    Int J Med Sci, 2015;12(1):23-31.
    PMID: 25552915 DOI: 10.7150/ijms.10019
    Lignosus rhinocerotis (Cooke) Ryvarden (Polyporales, Basidiomycota), also known as the tiger milk mushroom, has received much interest in recent years owing to its wide-range ethnobotanical uses and the recent success in its domestication. The sclerotium is the part with medicinal value. Using two-dimensional gel electrophoresis coupled with mass spectrometry analysis, a total of 16 non-redundant, major proteins were identified with high confidence level in L. rhinocerotis sclerotium based on its genome as custom mapping database. Some of these proteins, such as the putative lectins, immunomodulatory proteins, superoxide dismutase, and aegerolysin may have pharmaceutical potential; while others are involved in nutrient mobilization and the protective antioxidant mechanism in the sclerotium. The findings from this study provide a molecular basis for future research on potential pharmacologically active proteins of L. rhinocerotis.
    Matched MeSH terms: Proteomics/methods*
  20. A physicochemical investigation of membrane fouling in cold microfiltration of skim milk
    Tan TJ, Wang D, Moraru CI
    J Dairy Sci, 2014;97(8):4759-71.
    PMID: 24881794 DOI: 10.3168/jds.2014-7957
    The main challenge in microfiltration (MF) is membrane fouling, which leads to a significant decline in permeate flux and a change in membrane selectivity over time. This work aims to elucidate the mechanisms of membrane fouling in cold MF of skim milk by identifying and quantifying the proteins and minerals involved in external and internal membrane fouling. Microfiltration was conducted using a 1.4-μm ceramic membrane, at a temperature of 6±1°C, cross-flow velocity of 6m/s, and transmembrane pressure of 159kPa, for 90min. Internal and external foulants were extracted from a ceramic membrane both after a brief contact between the membrane and skim milk, to evaluate instantaneous adsorption of foulants, and after MF. Four foulant streams were collected: weakly attached external foulants, weakly attached internal foulants, strongly attached external foulants, and strongly attached internal foulants. Liquid chromatography coupled with tandem mass spectrometry analysis showed that all major milk proteins were present in all foulant streams. Proteins did appear to be the major cause of membrane fouling. Proteomics analysis of the foulants indicated elevated levels of serum proteins as compared with milk in the foulant fractions collected from the adsorption study. Caseins were preferentially introduced into the fouling layer during MF, when transmembrane pressure was applied, as confirmed both by proteomics and mineral analyses. The knowledge generated in this study advances the understanding of fouling mechanisms in cold MF of skim milk and can be used to identify solutions for minimizing membrane fouling and increasing the efficiency of milk MF.
    Matched MeSH terms: Proteomics/methods
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links