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Literature DB >> 24504115

Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery.

Robert Cunningham¹, Di Ma², Lingjun Li³.

Abstract

The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large datasets of proteins or peptides involved in various biological and disease progression processes producing testable hypothesis for complex biological questions. This review provides an introduction and insight to relevant topics in proteomics and peptidomics including biological material selection, sample preparation, separation techniques, peptide fragmentation, post-translation modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature and remaining challenges and emerging technologies for proteomics and peptidomics are presented.

Entities: CellLine Chemical Disease Gene Species

Keywords: Mass spectrometry; bioinformatics; biomarker discovery; fragmentation; peptidomics; post-translation modifications; protein quantitation; proteomics; review; sample preparation; separation; validation

Year: 2012 PMID： 24504115 PMCID： PMC3913178 DOI： 10.1007/s11515-012-1218-y

Source DB: PubMed Journal: Front Biol (Beijing) ISSN： 1674-7984

244 in total

Review 1. The regulation of protein function by multisite phosphorylation--a 25 year update.

Authors: P Cohen
Journal: Trends Biochem Sci Date: 2000-12 Impact factor: 13.807

2. Open mass spectrometry search algorithm.

Authors: Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal: J Proteome Res Date: 2004 Sep-Oct Impact factor: 4.466

3. Characterization of the human primary visual cortex and cerebellum proteomes using shotgun mass spectrometry-data-independent analyses.

Authors: Daniel Martins-de-Souza; Paul C Guest; Francesca L Guest; Corinna Bauder; Hassan Rahmoune; Sandra Pietsch; Sigrum Roeber; Hans Kretzschmar; David Mann; Atik Baborie; Sabine Bahn
Journal: Proteomics Date: 2012-01-10 Impact factor: 3.984

4. Mass spectrometric discovery and selective reaction monitoring (SRM) of putative protein biomarker candidates in first trimester Trisomy 21 maternal serum.

Authors: Mary F Lopez; Ramesh Kuppusamy; David A Sarracino; Amol Prakash; Michael Athanas; Bryan Krastins; Taha Rezai; Jennifer N Sutton; Scott Peterman; Kypros Nicolaides
Journal: J Proteome Res Date: 2010-06-04 Impact factor: 4.466

5. Quantitative analysis of human cerebrospinal fluid proteins using a combination of cysteine tagging and amine-reactive isobaric labeling.

Authors: Priscille Giron; Loïc Dayon; Natacha Turck; Christine Hoogland; Jean-Charles Sanchez
Journal: J Proteome Res Date: 2010-11-18 Impact factor: 4.466

6. Highly sensitive proteome analysis of FACS-sorted adult colon stem cells.

Authors: Serena Di Palma; Daniel Stange; Marc van de Wetering; Hans Clevers; Albert J R Heck; Shabaz Mohammed
Journal: J Proteome Res Date: 2011-07-08 Impact factor: 4.466

Review 7. Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specific biomarkers.

Authors: Paul Dowling; Martin Clynes
Journal: Proteomics Date: 2011-01-13 Impact factor: 3.984

8. Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches.

Authors: Mostafa Zarei; Adrian Sprenger; Fabian Metzger; Christine Gretzmeier; Joern Dengjel
Journal: J Proteome Res Date: 2011-07-08 Impact factor: 4.466

9. Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis.

Authors: A F Maarten Altelaar; Shabaz Mohammed; Maike A D Brans; Roger A H Adan; Albert J R Heck
Journal: J Proteome Res Date: 2009-02 Impact factor: 4.466

Review 10. Mass spectrometry-based label-free quantitative proteomics.

Authors: Wenhong Zhu; Jeffrey W Smith; Chun-Ming Huang
Journal: J Biomed Biotechnol Date: 2009-11-10

7 in total

1. Mechanistic peptidomics: factors that dictate specificity in the formation of endogenous peptides in human milk.

Authors: Andres Guerrero; David C Dallas; Stephanie Contreras; Sabrina Chee; Evan A Parker; Xin Sun; Lauren Dimapasoc; Daniela Barile; J Bruce German; Carlito B Lebrilla
Journal: Mol Cell Proteomics Date: 2014-08-29 Impact factor: 5.911

2. A Complete Mass Spectrometry (MS)-Based Peptidomic Description of Gluten Peptides Generated During In Vitro Gastrointestinal Digestion of Durum Wheat: Implication for Celiac Disease.

Authors: Fatma Boukid; Barbara Prandi; Andrea Faccini; Stefano Sforza
Journal: J Am Soc Mass Spectrom Date: 2019-05-02 Impact factor: 3.109

Review 3. Systematic Review and Meta-Analysis of Mass Spectrometry Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Schizophrenia.

Authors: João E Rodrigues; Ana Martinho; Catia Santa; Nuno Madeira; Manuel Coroa; Vítor Santos; Maria J Martins; Carlos N Pato; Antonio Macedo; Bruno Manadas
Journal: Int J Mol Sci Date: 2022-04-28 Impact factor: 6.208