J Integr Bioinform - On comparison of SimTandem with state-of-the-art peptide identification tools, efficiency of precursor mass filter and dealing with variable modifications.

Tópicos

{ search(2224) databas(1162) retriev(909) }
{ result(1111) use(1088) new(759) }
{ sequenc(1873) structur(1644) protein(1328) }
{ perform(999) metric(946) measur(919) }
{ model(2341) predict(2261) use(1141) }
{ cancer(2502) breast(956) screen(824) }
{ algorithm(1844) comput(1787) effici(935) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ drug(1928) target(777) effect(648) }
{ method(1969) cluster(1462) data(1082) }
{ can(774) often(719) complex(702) }
{ framework(1458) process(801) describ(734) }
{ data(1714) softwar(1251) tool(1186) }
{ howev(809) still(633) remain(590) }
{ import(1318) role(1303) understand(862) }
{ imag(1057) registr(996) error(939) }
{ assess(1506) score(1403) qualiti(1306) }
{ problem(2511) optim(1539) algorithm(950) }
{ clinic(1479) use(1117) guidelin(835) }
{ featur(1941) imag(1645) propos(1176) }
{ visual(1396) interact(850) tool(830) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ gene(2352) biolog(1181) express(1162) }
{ time(1939) patient(1703) rate(768) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ detect(2391) sensit(1101) algorithm(908) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ compound(1573) activ(1297) structur(1058) }
{ 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) }
{ model(2656) set(1616) predict(1553) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ patient(1821) servic(1111) care(1106) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ activ(1452) weight(1219) physic(1104) }
{ method(2212) result(1239) propos(1039) }

Resumo

The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.

Resumo Limpo

similar search theoret mass spectra generat protein sequenc databas wide accept approach identif peptid queri mass spectra produc shotgun proteom grow protein sequenc databas noisi queri spectra demand databas index techniqu better similar measur comparison theoret spectra queri spectra employ modif previous propos parameter hausdorff distanc comparison mass spectra new distanc outperform origin distanc angl distanc stateoftheart peptid identif tool omssa xtandem number identifi peptid even though qvalu precursor mass filter use databas index techniqu method outperform omssa speed search variabl modif search search time similar xtandem show precursor mass filter effici databas index techniqu highaccuraci data even though mani variabl modif search demonstr number identifi peptid bigger variabl modif search separ search run peptid identif engin otherwis fals discoveri rate affect mix unmodifi modifi spectra togeth result lower number identifi peptid method implement freeli avail applic simtandem can use framework topp base openm

Resumos Similares

J Chem Inf Model - Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods. ( 0,695154528918099 )
J Biomed Inform - A comparison of evaluation metrics for biomedical journals, articles, and websites in terms of sensitivity to topic. ( 0,684671389646274 )
J Biomed Inform - Development and evaluation of a biomedical search engine using a predicate-based vector space model. ( 0,675763745457141 )
J. Med. Internet Res. - Retrieving clinical evidence: a comparison of PubMed and Google Scholar for quick clinical searches. ( 0,673806420023962 )
Brief. Bioinformatics - Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. ( 0,672946403779753 )
J Integr Bioinform - The LAILAPS search engine: a feature model for relevance ranking in life science databases. ( 0,669245085054482 )
AMIA Annu Symp Proc - Does query expansion limit our learning? A comparison of social-based expansion to content-based expansion for medical queries on the internet. ( 0,659123369215686 )
Comput Biol Chem - An efficient similarity search based on indexing in large DNA databases. ( 0,657896730594057 )
Telemed J E Health - MEDLINE versus EMBASE and CINAHL for telemedicine searches. ( 0,646114742133359 )
Health Info Libr J - Medical literature searches: a comparison of PubMed and Google Scholar. ( 0,630323307329134 )
BMC Med Inform Decis Mak - CDAPubMed: a browser extension to retrieve EHR-based biomedical literature. ( 0,627018011304053 )
J. Med. Internet Res. - Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews. ( 0,626531384105934 )
J Biomed Inform - On the query reformulation technique for effective MEDLINE document retrieval. ( 0,625070522049096 )
J Biomed Inform - Knowledge-based personalized search engine for the Web-based Human Musculoskeletal System Resources (HMSR) in biomechanics. ( 0,625019348911412 )
Methods Inf Med - Technology-induced errors. The current use of frameworks and models from the biomedical and life sciences literatures. ( 0,624941811106442 )
J Am Med Inform Assoc - Search filters to identify geriatric medicine in Medline. ( 0,622983883785291 )
Health Info Libr J - Facilitating access to evidence: Primary Health Care Search Filter. ( 0,622314785260204 )
J. Med. Internet Res. - Development and validation of filters for the retrieval of studies of clinical examination from Medline. ( 0,620694957997269 )
J Am Med Inform Assoc - Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters. ( 0,613363795115285 )
J Integr Bioinform - Classification methods for finding articles describing protein-protein interactions in PubMed. ( 0,610944699498173 )
Brief. Bioinformatics - Fast and efficient searching of biological data resources--using EB-eye. ( 0,610149105213605 )
BMC Med Inform Decis Mak - Glomerular disease search filters for Pubmed, Ovid Medline, and Embase: a development and validation study. ( 0,60855062531534 )
Health Info Libr J - Utilisation of search filters in systematic reviews of prognosis questions. ( 0,602160328568695 )
Methods Inf Med - Learning the preferences of physicians for the organization of result lists of medical evidence articles. ( 0,602042747733808 )
AMIA Annu Symp Proc - Search filter precision can be improved by NOTing out irrelevant content. ( 0,601324432161361 )
J Telemed Telecare - How to improve your PubMed/MEDLINE searches: 1. background and basic searching. ( 0,60092333660741 )
J Integr Bioinform - A query suggestion workflow for life science IR-systems. ( 0,595167769687058 )
Health Info Libr J - The performance of adverse effects search filters in MEDLINE and EMBASE. ( 0,594973419338723 )
Health Info Libr J - Sensitivity and precision of adverse effects search filters in MEDLINE and EMBASE: a case study of fractures with thiazolidinediones. ( 0,594911631607124 )
J Am Med Inform Assoc - Leveraging medical thesauri and physician feedback for improving medical literature retrieval for case queries. ( 0,594154441517905 )
J Am Med Inform Assoc - MEDLINE clinical queries are robust when searching in recent publishing years. ( 0,592970067306974 )
J Integr Bioinform - The LAILAPS search engine: relevance ranking in life science databases. ( 0,592395389276606 )
BMC Med Inform Decis Mak - BOSS: context-enhanced search for biomedical objects. ( 0,591925762104005 )
Health Info Libr J - Where and how to search for information on the effectiveness of public health interventions - a case study for prevention of cardiovascular disease. ( 0,591841936839089 )
J Biomed Inform - A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. ( 0,589290418098099 )
J Chem Inf Model - Efficient substructure searching of large chemical libraries: the ABCD chemical cartridge. ( 0,587877881805175 )
J Integr Bioinform - GMB: an efficient query processor for biological data. ( 0,586465228529957 )
J Am Med Inform Assoc - Search terms and a validated brief search filter to retrieve publications on health-related values in Medline: a word frequency analysis study. ( 0,586428747811027 )
J Am Med Inform Assoc - DCMDSM: a DICOM decomposed storage model. ( 0,586129703619965 )
J Chem Inf Model - Subpocket analysis method for fragment-based drug discovery. ( 0,585627680111236 )
J Biomed Inform - MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms. ( 0,58490820097233 )
Perspect Health Inf Manag - Risk factors for bladder cancer: challenges of conducting a literature search using PubMed. ( 0,584020642487409 )
AMIA Annu Symp Proc - Evaluation of automated term groupings for detecting anaphylactic shock signals for drugs. ( 0,583506805674567 )
Int J Health Geogr - HEALTH GeoJunction: place-time-concept browsing of health publications. ( 0,58138801429246 )
J. Med. Internet Res. - Definition of Health 2.0 and Medicine 2.0: a systematic review. ( 0,580799208143643 )
J. Med. Internet Res. - Using Internet search engines to obtain medical information: a comparative study. ( 0,579365199890378 )
J Am Med Inform Assoc - A practical approach to achieve private medical record linkage in light of public resources. ( 0,579299508217985 )
Methods Inf Med - Developing topic-specific search filters for PubMed with click-through data. ( 0,579079855675366 )
AMIA Annu Symp Proc - BIOSPIDA: A Relational Database Translator for NCBI. ( 0,578176035783666 )
BMC Med Inform Decis Mak - Publication trends of shared decision making in 15 high impact medical journals: a full-text review with bibliometric analysis. ( 0,577932105324234 )
J Biomed Inform - Reflective random indexing for semi-automatic indexing of the biomedical literature. ( 0,57690374992991 )
BMC Med Inform Decis Mak - Boolean versus ranked querying for biomedical systematic reviews. ( 0,576127560669256 )
AMIA Annu Symp Proc - Predicting clicks of PubMed articles. ( 0,575682677305605 )
BMC Med Inform Decis Mak - Performance evaluation of Unified Medical Language System?'s synonyms expansion to query PubMed. ( 0,575593360299875 )
J Chem Inf Model - Scaffold hopping by fragment replacement. ( 0,571747689849207 )
Health Info Libr J - Developing a geographic search filter to identify randomised controlled trials in Africa: finding the optimal balance between sensitivity and precision. ( 0,568984183273744 )
Appl Clin Inform - Usability of selected databases for low-resource clinical decision support. ( 0,567501635521199 )
J. Med. Internet Res. - A search engine to access PubMed monolingual subsets: proof of concept and evaluation in French. ( 0,563528345264457 )
AMIA Annu Symp Proc - Optimizing the txt2MEDLINE search portal for low-resource clinical decision support. ( 0,56259290862261 )
Telemed J E Health - Should you search the Internet for information about your acute symptom? ( 0,562479490656742 )
IEEE Trans Vis Comput Graph - WORDGRAPH: Keyword-in-Context Visualization for NETSPEAK's Wildcard Search. ( 0,562412084340835 )
J Biomed Inform - Using statistical text mining to supplement the development of an ontology. ( 0,560591916135334 )
Health Info Libr J - Searching for randomised controlled trials and clinical controlled trials in Thai online bibliographical biomedical databases. ( 0,560534144111647 )
J Biomed Inform - Supporting effective health and biomedical information retrieval and navigation: a novel facet view interface evaluation. ( 0,559740008257107 )
J Biomed Inform - Improving search over Electronic Health Records using UMLS-based query expansion through random walks. ( 0,558035320386093 )
J. Comput. Biol. - LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value. ( 0,557819120195892 )
Int J Med Inform - FindZebra: a search engine for rare diseases. ( 0,555246853077978 )
J Med Syst - MIRASS: medical informatics research activity support system using information mashup network. ( 0,554542231112526 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,552402239207265 )
Inform Health Soc Care - Readability of online health information: implications for health literacy. ( 0,548541662557016 )
Artif Intell Med - Phased searching with NEAT in a time-scaled framework: experiments on a computer-aided detection system for lung nodules. ( 0,547939315249113 )
Comput Methods Programs Biomed - RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources. ( 0,546970484600777 )
Med Decis Making - A pilot study using machine learning and domain knowledge to facilitate comparative effectiveness review updating. ( 0,544821985494719 )
IEEE Trans Image Process - Short distance intra coding scheme for high efficiency video coding. ( 0,5442470716858 )
Health Info Libr J - Assessment of indexing trends with specific and general terms for herbal medicine. ( 0,542195981063535 )
AMIA Annu Symp Proc - Query log analysis of an electronic health record search engine. ( 0,541526523270872 )
Int J Med Inform - An analysis of clinical queries in an electronic health record search utility. ( 0,53766421266339 )
AMIA Annu Symp Proc - Using Co-Authoring and Cross-Referencing Information for MEDLINE Indexing. ( 0,537334960630471 )
J Am Med Inform Assoc - PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. ( 0,534734225865694 )
Res Synth Methods - Inquisitio validus Index Medicus: A simple method of validating MEDLINE systematic review searches. ( 0,53464791182035 )
Int J Med Inform - MEDRank: using graph-based concept ranking to index biomedical texts. ( 0,531244302559453 )
J Am Med Inform Assoc - Improving image retrieval effectiveness via query expansion using MeSH hierarchical structure. ( 0,528147954313782 )
J Am Med Inform Assoc - A literature search tool for intelligent extraction of disease-associated genes. ( 0,52666714574859 )
J. Med. Internet Res. - The impact of search engine selection and sorting criteria on vaccination beliefs and attitudes: two experiments manipulating Google output. ( 0,524524797807076 )
J Am Med Inform Assoc - Directing the public to evidence-based online content. ( 0,524383449166599 )
J Chem Inf Model - Searching for likeness in a database of macromolecular complexes. ( 0,523804838689663 )
J Am Med Inform Assoc - Clinical research data warehouse governance for distributed research networks in the USA: a systematic review of the literature. ( 0,523119011688665 )
Res Synth Methods - Comprehensive computer searches and reporting in systematic reviews. ( 0,520969127092523 )
BMC Med Inform Decis Mak - Harmonisation of variables names prior to conducting statistical analyses with multiple datasets: an automated approach. ( 0,518961485649595 )
J. Med. Internet Res. - Net improvement of correct answers to therapy questions after pubmed searches: pre/post comparison. ( 0,518121642136004 )
Brief. Bioinformatics - Adjusting confounders in ranking biomarkers: a model-based ROC approach. ( 0,517826210448254 )
BMC Med Inform Decis Mak - Pharmacoeconomics and its implication on priority-setting for essential medicines in Tanzania: a systematic review. ( 0,517214206616351 )
J Biomed Inform - A mutation-centric approach to identifying pharmacogenomic relations in text. ( 0,515979361238317 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,514888693635508 )
AMIA Annu Symp Proc - Author keywords in biomedical journal articles. ( 0,514744222844698 )
BMC Med Inform Decis Mak - Dynamic summarization of bibliographic-based data. ( 0,512049463518235 )
IEEE Trans Image Process - Fast query for exemplar-based image completion. ( 0,512039085693639 )
Comput Methods Programs Biomed - METRADISC-XL: a program for meta-analysis of multidimensional ranked discovery oriented datasets including microarrays. ( 0,512034780814413 )
J Chem Inf Model - Critical analysis of CCSD data quality. ( 0,509202569729806 )
Comput Biol Chem - Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1. ( 0,508112213251156 )