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Understanding the Proteomics of Medicinal Plants under Environmental Pollution
Published in Azamal Husen, Environmental Pollution and Medicinal Plants, 2022
Pooja Singh, V.K. Mishra, Rohit Kashyap, Rahul Rawat
Tandem MS (MS/MS) has been used to obtain the amino acid sequence of peptides. Peptide ions generated from an ESI source are separated based on the m/z ratio and further dissociated by collision with an inert gas (Mann et al. 2001). The resultant tandem spectra of amino acid composition can be searched against protein, expressed sequence tags (ESTs), and genome databases to identify the protein. Various programs used for tandem spectra are Sequest (Eng et al. 1994; Clauser et al. 1999), PROWL (Qin et al. 1997), Protein Prospector (Clauser et al. 1999), and MASCOT (Perkins et al. 1999).
Application of Genomic, Proteomic, and Metabolomic Technologies to the Development of Countermeasures against Chemical Warfare Agents
Published in Brian J. Lukey, James A. Romano, Salem Harry, Chemical Warfare Agents, 2019
Jennifer W. Sekowski, James F. Dillman III
The resulting MS-MS spectra represent the fragmentation patterns produced. The spectra provide fingerprints that define the sequence of peptide ions. Searching algorithms such as SEQUEST (http://fields.scripps.edu/sequest), Peptident (http://ca.expasy.org/tools), and MASCOT (http://matrixscience.com) makes the identification of proteins possible by correlating peptide MS-MS data with predicted MS-MS data generated from protein and nucleotide sequence databases. Automated LC-MS-MS scanning acquires MS-MS spectra for hundreds to thousands of peptides in a single LC analysis. The combination of data-dependent scanning and the use of search algorithms facilitates the identification of proteins from complex peptide mixtures using LC-MS-MS data. Combining MS-MS with reverse-phase or tandem LC (e.g., ion-exchange reverse phase) makes LC-MS-MS the most powerful approach for protein identification and characterization. Moreover, fragmentation of peptides using MS-MS provides unambiguous confirmation not only of sequence but also of the location and character of posttranslational modifications, protein adducts, and sequence variants (Loo et al., 1999).
Metabolomics and Proteomics
Published in Crystal D. Karakochuk, Kyly C. Whitfield, Tim J. Green, Klaus Kraemer, The Biology of the First 1,000 Days, 2017
Richard D. Semba, Marta Gonzalez-Freire
Bioinformatics has played a vital role in the acceleration of proteomics and metabolomics. Raw MS data from proteomic analyses can be analyzed using open source search engines such as X!Tandem and OMSSA, or proprietary databases such as Mascot and Sequest. The software assigns sequence information for peptides based upon the spectra, and then protein identifications based upon the specific peptides. Authoritative and comprehensive protein databases include neXtProt for human proteins [5]. Annotated databases such as Gene Ontology (GO) [17] and pathway databases such as Kyoto Encyclopedia of Genes and Genomes (KEGG) [18] and Database for Annotation, Visualization and Integrated Discovery (DAVID) [19] are particularly useful for the identification of biological pathways in the resulting data from proteomic and metabolomics investigations. Online resources and databases of metabolites include Metabolomics Workbench, METLIN, and BiGG [20].
De novo sequencing of proteins by mass spectrometry
Published in Expert Review of Proteomics, 2020
Rui Vitorino, Sofia Guedes, Fabio Trindade, Inês Correia, Gabriela Moura, Paulo Carvalho, Manuel A. S. Santos, Francisco Amado
There are various tools and software that assist researchers in the de novo sequencing of peptides. Most of these tools are freely available, whereas some are available under commercial licenses (Table 1). A peptide sequencing program based on the identification of positive ion peptides generated as a result of FAB was developed as early as 1986 [54]. PAAS 3 was one of the first programs to allow the MS-based identification of peptides and determination of their sequence information [36]. The tool is freely available. The program first generates all possible combinations of amino acids for a particular sequence, which are matched and searched against the reference spectrum. Lutefisk was one of the first de novo sequencing algorithms, which scans protein databases based on tandem mass spectra of trypsin-digested peptides [55]. Using the database, the algorithm applies graph theory and identifies several fragmented peptides that act as the query for a subsequent homology-based search. Mascot and SEQUEST are the two most widely used algorithms for MS/MS data interpretation. While SEQUEST is more commonly associated with ion trap MS/MS analyzers, Mascot is more often used in TOF analyzers [56]. Mascot uses a probabilistic model to assess the chances that a particular fragment is associated with the observed spectrum, while SEQUEST scores the observed and predicted spectra using correlation measures [57].
Zinc oxide nanoparticles induce murine photoreceptor cell death via mitochondria-related signaling pathway
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2018
Ling Wang, Chao Chen, Lijie Guo, Qin Li, Hongyan Ding, Hongsheng Bi, Dadong Guo
LC-MS/MS analysis was performed as previously described [24]. The datasets were obtained from three LC-MS/MS runs with three independent cell samples. For each resulting set of spectra, SEQUEST was used for peptide sequence assignment. Briefly, every sample was analyzed by Q-Exactive (Thermo Fisher Scientific, Waltham, MA) on a Thermo Scientific Easy-nLC 1000 system. The flow rate was set as 250 nL per min and the column temperature was set as 25 °C. After determination, database search was performed using Proteome Discoverer 1.3 software (Thermo Fisher Scientific Waltham, MA,) with SEQUEST search engine against Swiss-Prot protein sequence database. A two-tailed p values < .05 and a 1.5-fold alteration was regarded as the differentially expressed proteins. To obtain convincible data, three independent experiments of LC-MS/MS analysis were repeated. Every sample in each experiment was determined three times.
Proteomics and the microbiome: pitfalls and potential
Published in Expert Review of Proteomics, 2019
Huafeng Lin, Qing-Yu He, Lei Shi, Mark Sleeman, Mark S. Baker, Edouard C. Nice
The size and complexity of the data that can be generated means that bioinformatics is essential for data analysis. SEQUEST [117] is a commonly used search engine for searching MS data against human and microbial protein databases. A number of other useful open-source softwares and databases that are freely available include mMASS [118], Mass-Up [119], pkDACLASS [120], MALDIquant [121], SpectraBank [122] and BIOSPEAN [123]. Software tools including Pipasic [124], MetaProteome Analyzer [125], and Unipept [126] facilitate metaproteomic data analysis.