Bioinformatic challenges in targeted proteomics.
Summary of "Bioinformatic challenges in targeted proteomics."
Selected reaction monitoring mass spectrometry is an emerging targeted proteomics tech- nology that allows for the investigation of complex protein samples with high sensitivity and efficiency. It requires extensive knowledge about the sample for the many parameters needed to carry out the experiment to be set appropriately. Most studies today rely on parameter es- timation from prior studies, public databases or from measuring synthetic peptides. This is efficient and sound, but in absence of prior data, de novo parameter estimation is necessary. Computational methods can be used to create an automated framework to address this prob- lem. However, the number of available applications is still small. This review aims at giving an orientation on the various bioinformatical challenges. To this end, we state the problems in classical machine learning and data mining terms, give examples of implemented solutions and provide some room for alternatives. This will hopefully lead to an increased momentum for the development of algorithms and serve the needs of the community for computational methods. We note that the combination of such methods in an assisted workflow will ease both the usage of targeted proteomics in experimental studies as well as the further development of computational approaches.
Affiliation
Journal Details
This article was published in the following journal.
Name: Journal of proteome research
ISSN: 1535-3907
Pages:
Links
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/22866949
- DOI: http://dx.doi.org/10.1021/pr300276f
Medical and Biotech [MESH] Definitions
Radioimmunotherapy
Radiotherapy where cytotoxic radionuclides are linked to antibodies in order to deliver toxins directly to tumor targets. Therapy with targeted radiation rather than antibody-targeted toxins (IMMUNOTOXINS) has the advantage that adjacent tumor cells, which lack the appropriate antigenic determinants, can be destroyed by radiation cross-fire. Radioimmunotherapy is sometimes called targeted radiotherapy, but this latter term can also refer to radionuclides linked to non-immune molecules (see RADIOTHERAPY).
Adaptation, Physiological
The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.
Proteomics
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
Endometrial Ablation Techniques
Procedures used for the targeted destruction of the mucous membrane lining of the uterine cavity.
Targeted Gene Repair
A technique which uses synthetic oligonucleotides to direct the cell's inherent DNA repair system to correct a mutation at a specific site in an episome or chromosome.
PubMed Articles
Viewpoints in Clinical Proteomics - when will proteomics deliver clinically useful information?
Proteomics has not delivered biomarkers of clinical value, despite massive efforts. The technologies that are emerging today have, however, the power to reach deep into proteomes and to identify patte...
When peptides fly: advances in Drosophila proteomics.
In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the c...
Towards proteomics-on-chip: The role of the surface.
Miniaturisation is revolutionary to high-throughput proteomics. These technologies have gained much interest in the past decade, as they allow for sensitive parallel analysis of small amounts of biolo...
Multiclassifier proteomics to define complexes yields new chromosomal proteins.
In a recent issue of Cell, Ohta et al. report a method of quantitative proteomics coupled with bioinformatic analysis for the identification of associated components in complex mixtures. Using this a...
Clinical Trials
Pilot Study of Protein Profiling of the Human Epidermal Cells After Ultraviolet Irradiation
The main focus of this pilot study is to construct a fairly complete protein profile of the epidermis. This will allow us to study how the epidermis responds to external stressors such as...
Proteomics in Morbid Obesity After Bariatric Surgery
Glycemic control is rapidly restored in patients with insulin resistance after bariatric surgery, in particular after the mal-absorptive one (i.e. Bilio-pancreatic diversion, BPD). To ev...
RATIONALE: Diagnostic procedures, such as MRI, MRSI, and tissue proteomics, may help doctors find and diagnose breast cancer and plan the best treatment. PURPOSE: This clinical trial is s...
Tailored Messages to Increase Eye Examination Behavior
The purpose of this project is to test two different types of health messages, one that is developed for a specific group (targeted) and the other that is more personalized to individuals...
When a match related or matched unrelated donor is not available a Haploidentical donor (parent, sibling or child)is immediately available. The challenges associated with haploidentical HC...
