Comput. Biol. Med. - POTAMOS mass spectrometry calculator: computer aided mass spectrometry to the post-translational modifications of proteins. A focus on histones.

Tópicos

{ data(1714) softwar(1251) tool(1186) }
{ sequenc(1873) structur(1644) protein(1328) }
{ take(945) account(800) differ(722) }
{ structur(1116) can(940) graph(676) }
{ error(1145) method(1030) estim(1020) }
{ import(1318) role(1303) understand(862) }
{ cancer(2502) breast(956) screen(824) }
{ model(2656) set(1616) predict(1553) }
{ method(1969) cluster(1462) data(1082) }
{ system(1976) rule(880) can(841) }
{ bind(1733) structur(1185) ligand(1036) }
{ compound(1573) activ(1297) structur(1058) }
{ gene(2352) biolog(1181) express(1162) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ method(1557) propos(1049) approach(1037) }
{ patient(1821) servic(1111) care(1106) }
{ health(1844) social(1437) communiti(874) }
{ use(976) code(926) identifi(902) }
{ method(2212) result(1239) propos(1039) }
{ data(1737) use(1416) pattern(1282) }
{ measur(2081) correl(1212) valu(896) }
{ featur(3375) classif(2383) classifi(1994) }
{ framework(1458) process(801) describ(734) }
{ chang(1828) time(1643) increas(1301) }
{ care(1570) inform(1187) nurs(1089) }
{ studi(1410) differ(1259) use(1210) }
{ studi(1119) effect(1106) posit(819) }
{ cost(1906) reduc(1198) effect(832) }
{ data(3008) multipl(1320) sourc(1022) }
{ activ(1138) subject(705) human(624) }
{ can(981) present(881) function(850) }
{ drug(1928) target(777) effect(648) }
{ decis(3086) make(1611) patient(1517) }
{ detect(2391) sensit(1101) algorithm(908) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
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{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
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{ featur(1941) imag(1645) propos(1176) }
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{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ perform(1367) use(1326) method(1137) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ high(1669) rate(1365) level(1280) }
{ use(1733) differ(960) four(931) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }

Resumo

Mass spectrometry is a widely used technique for protein identification and it has also become the method of choice in order to detect and characterize the post-translational modifications (PTMs) of proteins. Many software tools have been developed to deal with this complication. In this paper we introduce a new, free and user friendly online software tool, named POTAMOS Mass Spectrometry Calculator, which was developed in the open source application framework Ruby on Rails. It can provide calculated mass spectrometry data in a time saving manner, independently of instrumentation. In this web application we have focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation, as suggested by the so called "histone code" hypothesis. The PTMs implemented in this software are: methylations of arginines and lysines, acetylations of lysines and phosphorylations of serines and threonines. The application is able to calculate the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass along with the full set of the unique primary structures produced by the possible distributions along the amino acid sequence. It can also calculate the masses and charges of a fragmented histone variant, which carries predefined modifications already implemented. Additional functionality is provided by the calculation of the masses of fragments produced upon protein cleavage by the proteolytic enzymes that are most widely used in proteomics studies.

Resumo Limpo

mass spectrometri wide use techniqu protein identif also becom method choic order detect character posttransl modif ptms protein mani softwar tool develop deal complic paper introduc new free user friend onlin softwar tool name potamo mass spectrometri calcul develop open sourc applic framework rubi rail can provid calcul mass spectrometri data time save manner independ instrument web applic focus well known protein famili histon whose ptms believ play crucial role gene regul suggest call histon code hypothesi ptms implement softwar methyl arginin lysin acetyl lysin phosphoryl serin threonin applic abl calcul kind number combin possibl ptms correspond given peptid sequenc given mass along full set uniqu primari structur produc possibl distribut along amino acid sequenc can also calcul mass charg fragment histon variant carri predefin modif alreadi implement addit function provid calcul mass fragment produc upon protein cleavag proteolyt enzym wide use proteom studi

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