From enjoy_your_dream1210_at_yahoo.co.jp Tue Jul 12 09:04:56 2005 Date: Tue, 12 Jul 2005 21:19:14 +0900 (JST) From: =?ISO-2022-JP?B?GyRCMGY+ZRsoQiAbJEJDaU06GyhC?= <enjoy_your_dream1210_at_yahoo.co.jp> Subject: Porcine protein database To: Multiple Recipients of <angenmap_at_animalgenome.org> Dear Sri/Madam; I am performing the proteomics research on porcine development and currently have a problem with protein identification after mass-spectrometry analysis of trypsin-digested peptides. I would like to know which database is the most suitable for protein search (database maching)? If anyone have an idea or advice, please give me any information. Thank you. Very sincerely yours, Tadao Tadao Inoue, M. D. 985 Sanzo, Higashimura-cho, Fukuyama, Hiroshima, 729-0292 Japan TEL: +81-84-936-2112 (4628) FAX: +81-84-936-2459 E-mail: enjoy_your_dream1210_at_yahoo.co.jp

From vallet_at_email.marc.usda.gov Fri Jul 15 14:48:33 2005 From: "Jeff Vallet" <vallet_at_email.marc.usda.gov> Subject: porcine protein database Date: Fri, 15 Jul 2005 13:45:12 -0500 To: Multiple Recipients of <angenmap_at_animalgenome.org> Dr. Inoue, When we do protein searches, we use the option that searches against all mammalian sequences. We have tried using the porcine EST sequences, but in our hands this information is not complete enough to provide a useful search. Using the mammalian sequences option and Mascot searching, for example, it is usually possible to get appropriate IDs. However, mass based searching such as Mascot, will often give the incorrect ID simply because the actual sequence of the protein is not present in the database, because the swine sequence database is incomplete, and homologous sequences from other species are not sufficiently identical to achieve a high enough score to produce a match. To deal with this problem, we do two types of searches, a Mascot or mass based search, and a homology tolerant search using MS-homology from protein prospector, which is available on the web. To do this type of search, we use the PEAKS program from Bioinformatics Solutions, Inc. to obtain de novo sequence information from the doubly charged peptides from our tandem mass spectrometry analysis of a given spot. Then, we submit all the de novo sequences from a particular spot to MS-homology in a batch. The homology tolerant search is not as dependent on an exact match as Mascot, and so it will often give an ID that is different from that of Mascot. Two thirds of the time, Mascot and MS-homology give the same ID, supporting the ID. For the other third of the time, we feel that MS-homology search, which is more tolerant of mismatches, is probably the better ID, but at least now have two alternative candidates for further research. Further details of our use of homology tolerant search methods can be found in Kayser et al., 2004, Journal of Biomolecular Techniques, 15:285-295. Jeffrey L. Vallet Research Leader USDA, ARS, Roman L. Hruska US Meat Animal Research Center PO Box 166 Clay Center, NE 68933 402-762-4187 FAX 402-762-4382

From enjoy_your_dream1210_at_yahoo.co.jp Thu Feb 16 01:23:19 2006 Date: Thu, 16 Feb 2006 16:23:19 +0900 (JST) From: =?ISO-2022-JP?B?GyRCMGY+ZRsoQiAbJEJDaU06GyhC?= <enjoy_your_dream1210_at_yahoo.co.jp> Subject: Porcine protein annotation To: Multiple Recipients of <angenmap_at_animalgenome.org> Hi, everyone, I am currently working on porcine proteome and handling hundreds of proteins of interest. I would like to categorize them into several groups on functional annotation (for example, protein synthesis group, metabolism group, membrane transport group, etc). Could anyone kindly please show me how this could be done? Very sincerely yours, Tadao ========================================== Tadao Inoue Department of Biotechnology, Fukuyama University 985 Sanzo, Higashimura-cho, Fukuyama, Hiroshima, 729-0292 Japan TEL: +81-84-936-2112 (4628) FAX: +81-84-936-2459 E-mail: enjoy_your_dream1210_at_yahoo.co.jp ===========================================

From zhu_at_iastate.edu Thu Feb 16 08:27:56 2006 Date: Thu, 16 Feb 2006 08:27:51 -0600 From: Zhiliang Hu <zhu_at_iastate.edu> Subject: Re: Porcine protein annotation To: Multiple Recipients of <angenmap_at_animalgenome.org> Tadao, If you can blast your proteins against the GO peptide db to obtain the GO ids for them, you can use the GO database/tools (http://www.geneontology.org/; "AmiGO", for example) to categorize them into "functional annotation" of your choice. If what you wanted was to get a simple count of appearance of your proteins within each of the "functional annotation", you can use my recently developed (http://www.animalgenome.org/bioinfo/resources/util/countgo.html) on-line tool -- currently this tool supports several commonly used "GO Slim" classifications such as GO_Slim, GOA, EGAD, etc. Good luck, Zhiliang /NAGRP Bioinformatics At 01:23 AM 2/16/2006, =?ISO-2022-JP?B?GyRCMGY+ZRsoQiAbJEJDaU06GyhC?= wrote: > Hi, everyone, > > I am currently working on porcine proteome and handling hundreds of proteins > of interest. I would like to categorize them into several groups on > functional annotation (for example, protein synthesis group, metabolism > group, membrane transport group, etc). Could anyone kindly please show me > how this could be done? > > Very sincerely yours, > > Tadao

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