Scientific Reports
| Autor: | Shreya Ahuja, Arba Karcini, Iulia M. Lazar, Carly Estrada-Palma |
|---|---|
| Přispěvatelé: | Biochemistry, Biological Sciences, Virginia Tech Carilion School of Medicine |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Sequence analysis lcsh:Medicine Peptide Breast Neoplasms Computational biology Biology Mass spectrometry Article 03 medical and health sciences 0302 clinical medicine Protein sequencing Breast cancer Protein methods Sequence Analysis Protein Tandem Mass Spectrometry medicine Humans Database search engine Amino Acid Sequence lcsh:Science Databases Protein Gene Proteogenomics chemistry.chemical_classification Multidisciplinary lcsh:R Cancer medicine.disease 3. Good health 030104 developmental biology chemistry lcsh:Q Peptides 030217 neurology & neurosurgery |
| Zdroj: | Scientific Reports Scientific Reports, Vol 9, Iss 1, Pp 1-13 (2019) |
| ISSN: | 2045-2322 |
| Popis: | Cancer evolves as a result of an accumulation of mutations and chromosomal aberrations. Developments in sequencing technologies have enabled the discovery and cataloguing of millions of such mutations. The identification of protein-level alterations, typically by using reversed-phase protein arrays or mass spectrometry, has lagged, however, behind gene and transcript-level observations. In this study, we report the use of mass spectrometry for detecting the presence of mutations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic MCF10A cells. The mutations were identified by expanding the database search process of raw mass spectrometry files by including an in-house built database of mutated peptides (XMAn-v1) that complemented a minimally redundant, canonical database of Homo sapiens proteins. The work resulted in the identification of nearly 300 mutated peptide sequences, of which ~50 were characterized by quality tandem mass spectra. We describe the criteria that were used to select the mutated peptide sequences, evaluate the parameters that characterized these peptides, and assess the artifacts that could have led to false peptide identifications. Further, we discuss the functional domains and biological processes that may be impacted by the observed peptide alterations, and how protein-level detection can support the efforts of identifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with identifier PXD014458. |
| Databáze: | OpenAIRE |
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