Shotgun Proteomics

Shotgun Proteomics General Details:

• "'Shotgun proteomics' refers to the direct analysis of complex protein mixtures to rapidly generate a global profile of the protein complement within the mixture." (Wu et al, 2002)
• The approach is enhanced by the use of multidimensional protein identification technology (MudPIT).
• MudPIT uses multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) & database-searching algorithms.
• Various algorithms can be used to increase the rate of confident peptide identifications, i.e. Percolator algorithm. (Käll L et al, 2007)
• Shotgun proteomics can also aid discovery of novel protein-coding genes, alternative splicing, & “resurrected” pseudogenes. (Florens & Washburn, 2006)

References:

• Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T (2011). Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome. Genome Res. 2011. 21: 756-767 [Full Text]
• Ding Y, Choi H, Nesvizhskii A. 2008. Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. J Proteome Res 7: 4878–4889.
• Florens L, Washburn MP. 2006. Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol. 2006;328:159-75.
• Käll L, Canterbury J, Weston J, Noble W, MacCoss M. 2007. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4: 923–925.
• Wu CC, MacCoss MJ. 2002. Shotgun proteomics: tools for the analysis of complex biological systems. Curr Opin Mol Ther. 2002 Jun;4(3):242-50.

Tags: Algorithm - Database Searching - HPLC - MudPIT - Proteomics - Shotgun Proteomics - Tandem Mass Spectrometry

Posted by Medicalchemy

Medicalchemy Group: History of Medicine - Images - Mnemonics - Syndromes - Acute Medicine - Anaesthesiology - Anatomy - Anthropology - Biochemistry - Cardiology - Dentistry - Dermatology - Drug ADR - Drugs - Embryology - Emergency Medicine - Endocrinology - Epidemiology - Family Medicine - Forensic Medicine - Gastroenterology - Genes - Genetics - Geriatrics - Gynecology - Haematology - Health Informatics - Hepatology - Immunology - Infection - Intensive Care - Medical Dictionary - Medical Education - Medical Statistics - Metabolic Medicine - Microbiology - Nephrology - Neuroanatomy - Neuroscience - Nuclear Medicine - Nutrition - Obstetrics - Occupational Health - Oncology - Ophthalmology - Orthopaedics - Otolaryngology - Paediatrics - Palliative Care - Parasitology - Pathology - Pharmacology - Physiology - Proteomics - Psychiatry - Public Health - Radiology - Respiratory - Rehabilitation - Rheumatology - Sports Medicine - Surgery - Toxicology - Tropical Medicine - Urology - Vascular - Virology.

Proteomics - The Study Of Proteins, Particularly Structure and Function

Proteomics - General Facts:

• The term "Proteome" comes from the blending of the words "Protein" & "Genome".
• An organism's proteome consists of it's entire complement of proteins.
• Proteomics deals with the large-scale study of proteins, especially structure & functions.
• After genomics, proteomics is considered the next essential area of study to facilitate the understanding of biological systems.

Proteomics - History:

• The term "proteomics" was first coined by Marc Wilkins in 1994, whilst a PhD student.[1]

Proteomics - Study Approaches:

• See Table.
• Broad-based approach - understand proteome as a whole.
• Focused approach - understand specific protein information.

Post-translational Modification Of Proteins:

• Acetylation
• Glycosylation
• Methylation
• Nitrosylation
• Oxidation
• Phosphorylation
• Ubiquitination

References:

[1] - UNSW Staff Bio: Professor Marc Wilkins (link)

Image: Table showing pros & cons of broad-based vrs focused approach to proteomics.

Image Credit: By Mccrearym on Wikipedia (public domain)

Tags: Acetylation - Genome - Genomics - Glycosylation - Methylation - Nitrosylation - Oxidation - Phosphorylation - Protein - Proteomics - Ubiquitination

Posted by Medicalchemy
Medicalchemy Group: History of Medicine - Images - Mnemonics - Syndromes - Acute Medicine - Anaesthesiology - Anatomy - Anthropology - Biochemistry - Cardiology - Dentistry - Dermatology - Drug ADR - Drugs - Embryology - Emergency Medicine - Endocrinology - Family Medicine - Forensic Medicine - Gastroenterology - Genes - Genetics - Geriatrics - Gynecology - Haematology - Health Informatics - Hepatology - Immunology - Infection - Intensive Care - Medical Education - Metabolic Medicine - Microbiology - Nephrology - Neuroanatomy - Neuroscience - Nuclear Medicine - Nutrition - Obstetrics - Occupational Health - Oncology - Ophthalmology - Orthopaedics - Otolaryngology - Paediatrics - Palliative Care - Parasitology - Pathology - Pharmacology - Physiology - Proteomics - Psychiatry - Public Health - Radiology - Respiratory - Rehabilitation - Rheumatology - Sports Medicine - Surgery - Toxicology - Tropical Medicine - Urology - Vascular - Virology.

Medicalchemy Proteomics Blog

This Medicalchemy (TM) blog will be about Proteomics related topics.

Tags: Blog - Proteins - Proteomics
Posted by Medicalchemy
Medicalchemy Group: History of Medicine - Images - Mnemonics - Syndromes - Acute Medicine - Anaesthesiology - Anatomy - Anthropology - Biochemistry - Cardiology - Dentistry - Dermatology - Drugs - Emergency Medicine - Endocrinology - Family Medicine - Forensic Medicine - Gastroenterology - Genes - Genetics - Geriatrics - Gynecology - Haematology - Health Informatics - Hepatology - Immunology - Infection - Intensive Care - Medical Education - Metabolic Medicine - Microbiology - Nephrology - Neuroanatomy - Neuroscience - Nuclear Medicine - Nutrition - Obstetrics - Occupational Health - Oncology - Ophthalmology - Orthopaedics - Otolaryngology - Paediatrics - Palliative Care - Parasitology - Pathology - Pharmacology - Physiology - Proteomics - Psychiatry - Public Health - Radiology - Respiratory - Rehabilitation - Rheumatology - Sports Medicine - Surgery - Toxicology - Tropical Medicine - Urology - Vascular - Virology.