Proteomics: a pragmatic perspective.

Nature Biotechnology
Parag Mallick, Bernhard Kuster

Abstract

The evolution of mass spectrometry-based proteomic technologies has advanced our understanding of the complex and dynamic nature of proteomes while concurrently revealing that no 'one-size-fits-all' proteomic strategy can be used to address all biological questions. Whereas some techniques, such as those for analyzing protein complexes, have matured and are broadly applied with great success, others, such as global quantitative protein expression profiling for biomarker discovery, are still confined to a few expert laboratories. In this Perspective, we attempt to distill the wide array of conceivable proteomic approaches into a compact canon of techniques suited to asking and answering specific types of biological questions. By discussing the relationship between the complexity of a biological sample and the difficulty of implementing the appropriate analysis approach, we contrast areas of proteomics broadly usable today with those that require significant technical and conceptual development. We hope to provide nonexperts with a guide for calibrating expectations of what can realistically be learned from a proteomics experiment and for gauging the planning and execution effort. We further provide a detailed supplement explaini...Continue Reading

References

Jul 1, 1995·Electrophoresis·V C WasingerI Humphery-Smith
Nov 8, 1996·Science·M R Emmert-BuckL A Liotta
Jan 21, 1997·Proceedings of the National Academy of Sciences of the United States of America·G NeubauerM Mann
Mar 14, 1997·The Journal of Biological Chemistry·P M RuddR A Dwek
Apr 16, 1998·Protein Science : a Publication of the Protein Society·A DucretR Aebersold
Dec 28, 1999·Proceedings of the National Academy of Sciences of the United States of America·Y LiuB F Cravatt
Nov 28, 2001·Analytical Chemistry·R ZhangF E Regnier
Feb 13, 2003·European Journal of Biochemistry·Andreas Bauer, Bernhard Kuster
Mar 1, 2003·Nature Biotechnology·Matthias Mann, Ole N Jensen
Mar 14, 2003·Nature·Ruedi Aebersold
Mar 20, 2003·Journal of Proteome Research·Roujian Zhang, Fred E Regnier
May 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·Scott A GerberSteven P Gygi
Oct 9, 2003·Molecular & Cellular Proteomics : MCP·Markus SchirleBernhard Kuster
Nov 20, 2003·Proteomics·Jun Ho Jang, Samir Hanash
Jan 27, 2004·Nature Cell Biology·Tewis BouwmeesterGiulio Superti-Furga
Feb 18, 2004·Mass Spectrometry Reviews·Joseph Zaia
Aug 6, 2004·Molecular & Cellular Proteomics : MCP·T P J DunkleyK S Lilley
Dec 14, 2004·Nature Biotechnology·John RushMichael J Comb
Jan 7, 2005·Nature·Jens S AndersenMatthias Mann
Jan 25, 2005·Molecular & Cellular Proteomics : MCP·Albrecht GruhlerOle N Jensen
Jan 28, 2005·Nature·E HoskinsonThomas M Haard
Feb 11, 2005·Current Opinion in Chemical Biology·Carilee DenisonSteven P Gygi
Feb 22, 2005·Methods : a Companion to Methods in Enzymology·Donald S KirkpatrickSteven P Gygi
Mar 3, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hanno SteenMarc W Kirschner
Mar 23, 2005·Nature Methods·Shao-En OngMatthias Mann
Jun 16, 2005·Nature Reviews. Molecular Cell Biology·Bernhard KusterRuedi Aebersold
Jul 15, 2005·Analytical Chemistry·Stephen TannerVineet Bafna

❮ Previous
Next ❯

Citations

Nov 1, 2011·Analytical and Bioanalytical Chemistry·Simone LemeerBernhard Kuster
May 31, 2012·Analytical and Bioanalytical Chemistry·Duangnapa KovanichAlbert J R Heck
Jul 10, 2012·Analytical and Bioanalytical Chemistry·Marcus BantscheffBernhard Kuster
Dec 5, 2012·Analytical and Bioanalytical Chemistry·Yu LiangYukui Zhang
Sep 5, 2012·Glycoconjugate Journal·Milos V NovotnyBenjamin F Mann
Apr 8, 2011·Journal of the American Society for Mass Spectrometry·Thangiah GeethaZhengping Yi
Feb 22, 2012·Parasitology·Karl Burgess, Richard Burchmore
Sep 25, 2012·Journal of Proteome Research·Annette MichalskiMatthias Mann
Jul 24, 2013·Journal of Proteome Research·Jiyang ZhangHongwei Xie
May 1, 2013·Journal of Proteome Research·Harald MarxBernhard Kuster
Jun 26, 2013·Journal of Proteome Research·Fiona PachlBernhard Kuster
Jul 14, 2010·Nature Biotechnology·Bruno Domon, Ruedi Aebersold
Mar 14, 2012·Nature Reviews. Genetics·Christine Vogel, Edward M Marcotte
Jun 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Stephen T DeyrupFrank C Schroeder
Feb 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Yariv WineGeorge Georgiou
Oct 1, 2011·Molecular & Cellular Proteomics : MCP·Zhixiang WuBernhard Kuster
Feb 4, 2012·Molecular & Cellular Proteomics : MCP·Christoph SchaabMatthias Mann
Mar 24, 2012·Molecular & Cellular Proteomics : MCP·Sally J DeebMatthias Mann
Oct 22, 2013·Molecular & Cellular Proteomics : MCP·Alexander S HebertJoshua J Coon
Aug 7, 2012·Molecular & Cellular Proteomics : MCP·Amelia C PetersonJoshua J Coon
Dec 20, 2012·Molecular & Cellular Proteomics : MCP·Sven NahnsenOliver Kohlbacher
Dec 4, 2012·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Jun 7, 2012·Nucleic Acids Research·Jean-Philippe GagnéGuy G Poirier
Oct 26, 2012·Retina·Jessica M SkeieVinit B Mahajan
Sep 14, 2012·Mediators of Inflammation·Martina AngiMario R Romano
Apr 19, 2012·Circulation. Cardiovascular Genetics·Diana Klingler, Markus Hardt
Dec 7, 2011·PLoS Computational Biology·Lukas Käll, Olga Vitek
Aug 27, 2013·PloS One·Anida SarajlićNataša Pržulj
Aug 2, 2013·Avian Diseases·Dusan Kunec
Dec 4, 2012·International Journal of Molecular Sciences·Rocco SavinoRosa Terracciano
Jun 1, 2012·The Journal of Nutrition·Donato F Romagnolo, John A Milner
Jan 3, 2012·International Journal of Biological Sciences·Young-Man KimJong Hwa Yum
Feb 8, 2013·Biomarkers in Medicine·Kay Ohlendieck
Sep 24, 2013·Experimental Eye Research·Pathma RamasamyPaula Meleady
Apr 9, 2011·Biomarkers in Medicine·Larry GoldFintan Steele

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.