Complementary methods to assist subcellular fractionation in organellar proteomics.

Abstract:

:Organellar proteomics aims to describe the full complement of proteins of subcellular structures and organelles. When compared with whole-cell or whole-tissue proteomes, the more focused results from subcellular proteomic studies have yielded relatively simpler datasets from which biologically relevant information can be more easily extracted. In every proteomic study, the quality and purity of the biological sample to be investigated is of the utmost importance for a successful analysis. In organellar proteomics, one of the most crucial steps in sample preparation is the initial subcellular fractionation procedure by which the enriched preparation of the sought-after organelle is obtained. In nearly all available organellar proteomic studies, the method of choice relies on one or several rounds of density-based gradient centrifugation. Although this method has been recognized for decades as yielding relatively pure preparations of organelles, recent technological advances in protein separation and identification can now reveal even minute amounts of contamination, which in turn can greatly complicate data interpretation. The scope of this review focuses on recently published innovative complementary or alternative methods to perform subcellular fractionation, which can further refine the way in which sample preparation is accomplished in organellar proteomics.

journal_name

Expert Rev Proteomics

authors

Gauthier DJ,Lazure C

doi

10.1586/14789450.5.4.603

subject

Has Abstract

pub_date

2008-08-01 00:00:00

pages

603-17

issue

4

eissn

1478-9450

issn

1744-8387

journal_volume

5

pub_type

杂志文章,评审
  • Proximity ligation assays: a recent addition to the proteomics toolbox.

    abstract::An essential skill for every researcher is to learn how to select and apply the most appropriate methods for the questions they are trying to answer. With the extensive variety of methods available, it is increasingly important to scrutinize the advantages and disadvantages of these techniques prior to making a decisi...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/epr.10.10

    authors: Weibrecht I,Leuchowius KJ,Clausson CM,Conze T,Jarvius M,Howell WM,Kamali-Moghaddam M,Söderberg O

    更新日期:2010-06-01 00:00:00

  • Integrated analysis of genetic, genomic and proteomic data.

    abstract::The rapid expansion of methods for measuring biological data ranging from DNA sequence variations to mRNA expression and protein abundance presents the opportunity to utilize multiple types of information jointly in the study of human health and disease. Organisms are complex systems that integrate inputs at myriad le...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.1.1.67

    authors: Reif DM,White BC,Moore JH

    更新日期:2004-06-01 00:00:00

  • Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics.

    abstract::There is a wealth of knowledge in the field of in vitro diagnostics with regard to preanalytical variables and their impact on the determination of peptide and protein analytes in human serum and plasma. This information is applicable to clinical proteomics investigations, which utilize the same sample types. Studies ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.3.4.409

    authors: Rai AJ,Vitzthum F

    更新日期:2006-08-01 00:00:00

  • Proteomics of proteasome complexes and ubiquitinated proteins.

    abstract::Ubiquitin-proteasome-mediated protein degradation is central to the regulation of many important biological processes, including cell cycle progression, apoptosis and DNA repair. Recognition and degradation of ubiquitinated substrates by the 26S proteasome is tightly regulated to maintain normal cell growth. Disruptio...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.4.5.649

    authors: Wang X,Guerrero C,Kaiser P,Huang L

    更新日期:2007-10-01 00:00:00

  • Recent mass spectrometry-based proteomics for biomarker discovery in lung cancer, COPD, and asthma.

    abstract:INTRODUCTION:Lung cancer and related diseases have been one of the most common causes of deaths worldwide. Genomic-based biomarkers may hardly reflect the underlying dynamic molecular mechanism of functional protein interactions, which is the center of a disease. Recent developments in mass spectrometry (MS) have made ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1080/14789450.2017.1304215

    authors: Fujii K,Nakamura H,Nishimura T

    更新日期:2017-04-01 00:00:00

  • A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

    abstract::The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章

    doi:10.1080/14789450.2017.1339604

    authors: Gadher SJ,Drahos L,Vékey K,Kovarova H

    更新日期:2017-07-01 00:00:00

  • The SODyssey: superoxide dismutases from biochemistry, through proteomics, to oxidative stress, aging and nutraceuticals.

    abstract::A total of 40 years have already passed since the pioneering work of McCord and Fridovich on erythrocuprein superoxide dismutase (SOD) activity. This modern scientific 'Odyssey' has been accompanied by a series of successes in the fields of biochemistry, biomedicine and proteomics. In this article, we resume the main ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/epr.11.13

    authors: D'Alessandro A,Zolla L

    更新日期:2011-06-01 00:00:00

  • Proteomic analysis in allergy and intolerance to wheat products.

    abstract::Owing to its extensive use in the human diet, wheat is among the most common causes of food-related allergies and intolerances. Allergies to wheat are provoked by ingestion, inhalation or contact with either the soluble or the insoluble gluten proteins in wheat. Gluten proteins, and particularly the gliadin fraction, ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/epr.10.98

    authors: Mamone G,Picariello G,Addeo F,Ferranti P

    更新日期:2011-02-01 00:00:00

  • Plasma hepcidin in early-stage breast cancer patients: no relationship with interleukin-6, erythropoietin and erythroferrone.

    abstract:OBJECTIVE:Hepcidin-25 production is stimulated by systemic inflammation, and it interferes with iron utilization, leading to anemia. This study aimed to investigate the relationships between the plasma levels of hepcidin, interleukin-6 (IL-6), erythropoietin (EPO) and erythroferrone (ERFE) in patients with benign breas...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章

    doi:10.1586/14789450.2015.1099436

    authors: Ciniselli CM,De Bortoli M,Taverna E,Varinelli L,Pizzamiglio S,Veneroni S,Bonini C,Orlandi R,Verderio P,Bongarzone I

    更新日期:2015-01-01 00:00:00

  • Dissecting phosphorylation networks: lessons learned from yeast.

    abstract::Protein phosphorylation continues to be regarded as one of the most important post-translational modifications found in eukaryotes and has been implicated in key roles in the development of a number of human diseases. In order to elucidate roles for the 518 human kinases, phosphorylation has routinely been studied usi...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/epr.11.64

    authors: Mok J,Zhu X,Snyder M

    更新日期:2011-12-01 00:00:00

  • Strategies in mass spectrometry for the assignment of Cys-Cys disulfide connectivities in proteins.

    abstract::Elucidating disulfide linkage patterns is a crucial part of protein characterization, for which mass spectrometry (MS) is now an indispensable analytical tool. In many cases, MS-based disulfide connectivity assignment is straightforwardly achieved using one-step protein fragmentation in the unreduced form followed by ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.2013.837663

    authors: Goyder MS,Rebeaud F,Pfeifer ME,Kálmán F

    更新日期:2013-10-01 00:00:00

  • Mass spectrometric approaches for characterizing bacterial proteomes.

    abstract::The emergence of advanced liquid chromatography mass spectrometry technologies for characterizing very complex mixtures of proteins has greatly propelled the field of proteomics, the goal of which is the simultaneous examination of all the proteins expressed by an organism. This research area represents a paradigm shi...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.1.4.433

    authors: VerBerkmoes NC,Connelly HM,Pan C,Hettich RL

    更新日期:2004-12-01 00:00:00

  • Proteomics advances for precision therapy in ovarian cancer.

    abstract::Introduction: Due to the relatively low mutation rate and high frequency of copy number variation, finding actionable genetic drivers of high-grade serous carcinoma (HGSC) is a challenging task. Furthermore, emerging studies show that genetic alterations are frequently poorly represented at the protein level adding a ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1080/14789450.2019.1666004

    authors: Labrie M,Kendsersky ND,Ma H,Campbell L,Eng J,Chin K,Mills GB

    更新日期:2019-10-01 00:00:00

  • Improved understanding of gene expression regulation using systems biology.

    abstract::This article reviews the current state of systems biology approaches, including the experimental tools used to generate 'omic' data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.2.6.915

    authors: Kuczenski RS,Aggarwal K,Lee KH

    更新日期:2005-12-01 00:00:00

  • Regulation of gene expression: probing DNA-protein interactions in vivo and in vitro.

    abstract::Tremendous efforts have been put together over the last several years to complete the entire sequencing of the human genome. As we enter the proteomic era, when the major aim is understanding which gene encodes which protein, the time has also come to identify their precise function inside the astonishing signaling ne...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.2.5.705

    authors: Vigneault F,Guérin SL

    更新日期:2005-10-01 00:00:00

  • An update on the routine application of MALDI-TOF MS in clinical microbiology.

    abstract::Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has entered clinical diagnostics and is today a generally accepted and integral part of the workflow for microbial identification. MALDI-TOF MS identification systems received approval from national and internatio...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章

    doi:10.1080/14789450.2019.1645603

    authors: Welker M,Van Belkum A,Girard V,Charrier JP,Pincus D

    更新日期:2019-08-01 00:00:00

  • Proteomics in studying cancer stem cell biology.

    abstract::Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and ho...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/epr.12.24

    authors: Kranenburg O,Emmink BL,Knol J,van Houdt WJ,Rinkes IH,Jimenez CR

    更新日期:2012-06-01 00:00:00

  • Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach.

    abstract::Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1080/14789450.2019.1654860

    authors: Min CW,Gupta R,Agrawal GK,Rakwal R,Kim ST

    更新日期:2019-09-01 00:00:00

  • Shining a light on defective autophagy by proteomics approaches: implications for neurodegenerative illnesses.

    abstract::Introduction: Autophagy is one of the most conserved clearance systems through which eukaryotes manage to handle dysfunctional and excess organelles and macromolecules. This catabolic process has not only a role in the maintenance of basal turnover of cellular components, but it is also essential in cells adaptation t...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1080/14789450.2019.1691919

    authors: Di Domenico F,Zuliani I,Tramutola A

    更新日期:2019-01-01 00:00:00

  • Investigation of therapy resistance mechanisms in myeloid leukemia by protein profiling of bone marrow extracellular fluid.

    abstract::In spite of the effective chronic myeloid leukemia (CML) therapy, a small percentage will fail on therapy and develop acute myeloid leukemia-like blast crisis. Understanding the underlying biology of therapy resistance is probably needed to develop better blood cancer therapy, and CML may be an ideal disease model for...

    journal_title:Expert review of proteomics

    pub_type: 评论,杂志文章

    doi:10.1586/epr.12.55

    authors: Gjertsen BT,Wiig H

    更新日期:2012-12-01 00:00:00

  • Transcriptional control and transcriptomic analysis of lipid metabolism in skin barrier formation and atopic dermatitis (AD).

    abstract::Introduction: Atopic dermatitis (AD) is a multifactorial ailment associated with barrier breach and intense systemic inflammation. Several studies over the years have shown the complex interplay of a large number of factors in governing the progression and outcome of AD. In addition to the diverse types of AD resultin...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章

    doi:10.1080/14789450.2019.1646128

    authors: Bhattacharya N,Ganguli-Indra G,Indra AK

    更新日期:2019-08-01 00:00:00

  • Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis.

    abstract:INTRODUCTION:The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibi...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1080/14789450.2017.1353912

    authors: Mourino-Alvarez L,Baldan-Martin M,Rincon R,Martin-Rojas T,Corbacho-Alonso N,Sastre-Oliva T,Barderas MG

    更新日期:2017-08-01 00:00:00

  • Understanding type 1 diabetes through proteomics.

    abstract:INTRODUCTION:Auto-immunity against pancreatic beta-cells leads to an absolute shortage of the hormone insulin, resulting in hyperglycemia and the onset of type 1 diabetes (T1D). Proteomic approaches have been used to elucidate the mechanisms of beta-cell dysfunction and death. Areas covered: In the present review, we d...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1080/14789450.2017.1345633

    authors: Crèvecoeur I,Vig S,Mathieu C,Overbergh L

    更新日期:2017-07-01 00:00:00

  • Surface plasmon resonance mass spectrometry in proteomics.

    abstract::Due to the enormous complexity of the proteome, focus in proteomics shifts more and more from the study of the complete proteome to the targeted analysis of part of the proteome. The isolation of this specific part of the proteome generally includes an affinity-based enrichment. Surface plasmon resonance (SPR), a labe...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.5.3.425

    authors: Visser NF,Heck AJ

    更新日期:2008-06-01 00:00:00

  • Advances in cell-free protein array methods.

    abstract:INTRODUCTION:Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, t...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章

    doi:10.1080/14789450.2018.1415146

    authors: Yu X,Petritis B,Duan H,Xu D,LaBaer J

    更新日期:2018-01-01 00:00:00

  • A huntingtin-HAP1-PCM1 pathway in ciliogenesis.

    abstract::Huntington's disease (HD) is caused by expansion of a polyglutamine repeat in the N-terminal region of huntingtin (htt), a large protein that has been found to interact with a variety of proteins. It remains to be determined how the interactions of htt with other proteins are involved in the pathogenesis of HD. A rece...

    journal_title:Expert review of proteomics

    pub_type: 评论,杂志文章

    doi:10.1586/epr.11.72

    authors: Li S,Li XJ

    更新日期:2012-01-01 00:00:00

  • The human urinary exosome as a potential metabolic effector cargo.

    abstract::Exosomes are nanovesicles, derived from the endocytic pathway, released by most cell types and found in many body fluids, including urine. A variety of exosomal functions have been reported, including transfer of RNA, cell communication, control of apoptosis and protein lifespan. Exosomes from mesenchymal stem cells c...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.2015.1055324

    authors: Bruschi M,Ravera S,Santucci L,Candiano G,Bartolucci M,Calzia D,Lavarello C,Inglese E,Petretto A,Ghiggeri G,Panfoli I

    更新日期:2015-08-01 00:00:00

  • 2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases.

    abstract::This review addresses the challenges of neuroproteomics and recent progress in biomarkers and tests for neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. The review will discuss how the application of quantitative 2D gel electrophoresis, combined with app...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.3.1.45

    authors: Sheta EA,Appel SH,Goldknopf IL

    更新日期:2006-02-01 00:00:00

  • Proteomics of neural stem cells.

    abstract::The isolation of neural stem cells from fetal and adult mammalian CNS and the demonstration of functional neurogenesis in adult CNS have offered perspectives for treatment of many devastating hereditary and acquired neurological diseases. Due to this enormous potential, neural stem cells are a subject of extensive mol...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章,评审

    doi:10.1586/14789450.5.2.175

    authors: Skalnikova H,Vodicka P,Gadher SJ,Kovarova H

    更新日期:2008-04-01 00:00:00

  • Transcriptomic profiling in Cutaneous Leishmaniasis patients.

    abstract:INTRODUCTION:Cutaneous leishmaniasis (CL), caused by different Leishmania parasite species, is associated with parasite-induced immune-mediated skin inflammation and ulceration. Whereas many CL studies focus on gene expression signatures in mouse models, the transcriptional response driving human patients in the field ...

    journal_title:Expert review of proteomics

    pub_type: 杂志文章

    doi:10.1080/14789450.2020.1812390

    authors: Masoudzadeh N,Mizbani A,Rafati S

    更新日期:2020-01-01 00:00:00