Modern strategies for protein quantification in proteome analysis: Advantages and limitations

Hamdan, Mahmoud; Righetti, Pier Giorgio

doi:10.1002/mas.10032

Cited by 130 publications

(95 citation statements)

References 51 publications

(49 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additional information on CWP can be obtained using methods already developed in proteomic approaches for improving the extraction of CWP strongly bound to cell wall components, such as polysaccharides or lignins, and/or the separation of CWP prior, to identification by mass spectrometry [63,64]. Since quantitative data are still missing, accurate comparisons between samples can be pursued by applying available techniques to perform differential proteomics [65,66]. The understanding of the biochemical and/or biological functions of proteins, increasingly calls for the fine characterization of CWP [37,67].…”

Section: Discussionmentioning

confidence: 99%

Cell wall proteins: a new insight through proteomics

Jamet

Canut

Boudart

et al. 2006

Trends in Plant Science

251

211

View full text Add to dashboard Cite

Cell wall proteins (CWP) are essential constituents of plant cell walls involved in modifications of cell wall components, wall structure, signaling, and interactions with plasma membrane proteins at the cell surface. The application of proteomic approaches to the cell wall compartment raises important questions: Are there technical problems specific to cell wall proteomics? What kinds of proteins can be found in Arabidopsis walls? Are some of them unexpected? What sort of post-translational modifications have so far been characterized in CWP? The purpose of this review is to discuss the experimental results obtained so far using protomics, as well as some of the new questions challenging future research. Glossary AGP (arabinogalactan proteins):cell wall highly glycosylated HRGP that contain repetitive motifs such as (Ser, Thr, Ala)-Hyp-(Ser, Thr, Ala)-Hyp or (Ser, Thr, Ala)-Hyp-Hyp. AG (arabinogalactan)-peptides: AGP that have a predicted mature protein backbone of 10 to 13 amino acid residues. BBE: berberine-bridge (S)-reticulin:oxygen oxidoreductases. CWP: cell wall proteins. Extensins: cell wall structural HRGP, with numerous Ser-Hyp n (n≥3) motifs separated by Tyr-, Lys-, His-and Val-rich regions. GAP (glycosylphosphatidylinositol anchored proteins): proteins that are lipid-anchored to the external phase of the plasma membrane. GH (glycoside hydrolases): enzymes that hydrolyze the glycosidic bond between two carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. HRGP: hydroxyproline-rich glycoproteins, i.e. extensins and AGP. Lectins: structurally diverse proteins that bind to specific carbohydrates. LRR (leucine-rich repeat): short sequence motifs having diverse functions and cellular locations, usually involved in protein-protein interactions. PME (pectin methylesterases): enzymes that catalyze the de-esterification of pectin into pectate and methanol. Proteome: the complete profile of proteins expressed, at a given time and environmental conditions, in a given organ, tissue, or cell. PRP (proline-rich proteins): structural CWP rich in proline residues. Transcriptome: the complete collection of transcribed elements of the genome.

show abstract

Section: Discussionmentioning

confidence: 99%

Cell wall proteins: a new insight through proteomics

Jamet

Canut

Boudart

et al. 2006

Trends in Plant Science

251

211

View full text Add to dashboard Cite

show abstract

“…Through these and other recent developments mass spectrometry has become a well-accepted and increasingly important technology in proteomics (protein identification and quantification, protein profiling, and protein interactions) (Hamdan & Righetti, 2002;Mo & Karger, 2002;Aebersold & Mann, 2003). The proteomics-based mass spectrometry techniques provide information on the molecular masses of proteins and their primary sequences, but do not directly provide any information on higher order protein structures and interactions.…”

Section: Introductionmentioning

confidence: 99%

Investigation of intact protein complexes by mass spectrometry

Heck

Heuvel

2004

Mass Spectrometry Reviews

553

554

View full text Add to dashboard Cite

I. Introduction 00 II. Electrospray Ionization of Biomacromolecules 00 III. Mass Analyzers for Biomacromolecular Mass Spectrometry 00 A. Collisional Cooling and/or Focusing 00 B. Alternative Mass Analyzers 00 IV. Solution‐Phase Properties of Proteins Complexes 00 A. Protein–Protein Interactions 00 B. Cooperativity and Cofactors 00 C. Dynamics of Assembly 00 V. Gas‐Phase Properties of Protein Complexes 00 A. Tandem Mass Spectrometry 00 B. Charge Separation in Protein Dissociation 00 VI. Future Outlook 00 Acknowledgments 00 References 00 Mass spectrometry has grown in recent years to a well‐accepted and increasingly important complementary technique in structural biology. Especially electrospray ionization mass spectrometry is well suited for the detection of non‐covalent protein complexes and their interactions with DNA, RNA, ligands, and cofactors. Over the last decade, significant advances have been made in the ionization and mass analysis techniques, which makes the investigation of even larger and more heterogeneous intact assemblies feasible. These technological developments have paved the way to study intact non‐covalent protein–protein interactions, assembly and disassembly in real time, subunit exchange, cooperativity effects, and effects of cofactors, allowing us a better understanding of proteins in cellular processes. In this review, we describe some of the latest developments and several highlights. © 2004 Wiley Periodicals, Inc., Mass Spec Rev

show abstract

“…This includes 2-DE-based methods such as the 2-D difference gel electrophoresis (DIGE) [69] and the development of sensitive fluorescent dyes with an increased dynamic range [70,71]. Likely more important are isotope coded protein-labeling techniques that allow MS-based strategies for protein quantification [72][73][74] (reviewed in [75]). …”

Section: Proteomics Technologiesmentioning

confidence: 99%

Neuroproteomics – the tasks lying ahead

2006

View full text Add to dashboard Cite

The brain is unquestionably the most fascinating organ. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward improved understanding of the molecular mechanisms underlying brain function is neuroproteomics. Today's neuroscientists have access to a battery of versatile technologies both in transcriptomics and proteomics. The challenge is to choose the right strategy in order to generate new hypotheses on how the brain works. The goal of this review is therefore two-fold: first we recall the bewildering cellular, molecular, and functional complexity in the brain, as this knowledge is fundamental to any study design. In fact, an impressive complexity on the molecular level has recently re-emerged as a central theme in large-scale analyses. Then we review transcriptomics and proteomics technologies, as both are complementary. Finally, we comment on the most widely used proteomics techniques and their respective strengths and drawbacks. We conclude that for the time being, neuroproteomics should focus on its strengths, namely the identification of posttranslational modifications and protein-protein interactions, as well as the characterization of highly purified subproteomes. For global expression profiling, emphasis should be put on further development to significantly increase coverage.

show abstract

Modern strategies for protein quantification in proteome analysis: Advantages and limitations

Cited by 130 publications

References 51 publications

Cell wall proteins: a new insight through proteomics

Cell wall proteins: a new insight through proteomics

Investigation of intact protein complexes by mass spectrometry

Neuroproteomics – the tasks lying ahead

Contact Info

Product

Resources

About