J. Comput. Biol. - Shape-based feature matching improves protein identification via LC-MS and tandem MS.

Tópicos

{ method(1219) similar(1157) match(930) }
{ featur(1941) imag(1645) propos(1176) }
{ detect(2391) sensit(1101) algorithm(908) }
{ assess(1506) score(1403) qualiti(1306) }
{ first(2504) two(1366) second(1323) }
{ estim(2440) model(1874) function(577) }
{ spatial(1525) area(1432) region(1030) }
{ sampl(1606) size(1419) use(1276) }
{ patient(2837) hospit(1953) medic(668) }
{ data(3008) multipl(1320) sourc(1022) }
{ cancer(2502) breast(956) screen(824) }
{ inform(2794) health(2639) internet(1427) }
{ sequenc(1873) structur(1644) protein(1328) }
{ visual(1396) interact(850) tool(830) }
{ can(981) present(881) function(850) }
{ take(945) account(800) differ(722) }
{ algorithm(1844) comput(1787) effici(935) }
{ data(1714) softwar(1251) tool(1186) }
{ research(1085) discuss(1038) issu(1018) }
{ compound(1573) activ(1297) structur(1058) }
{ studi(1119) effect(1106) posit(819) }
{ data(2317) use(1299) case(1017) }
{ analysi(2126) use(1163) compon(1037) }
{ high(1669) rate(1365) level(1280) }
{ can(774) often(719) complex(702) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ studi(2440) review(1878) systemat(933) }
{ error(1145) method(1030) estim(1020) }
{ extract(1171) text(1153) clinic(932) }
{ design(1359) user(1324) use(1319) }
{ method(984) reconstruct(947) comput(926) }
{ howev(809) still(633) remain(590) }
{ import(1318) role(1303) understand(862) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ state(1844) use(1261) util(961) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ bind(1733) structur(1185) ligand(1036) }
{ 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) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ method(1557) propos(1049) approach(1037) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
{ blood(1257) pressur(1144) flow(957) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ model(2656) set(1616) predict(1553) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ gene(2352) biolog(1181) express(1162) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

The characterization of proteins via liquid chromatography-mass spectrometry (LC-MS) and tandem MS is a challenge due to the large dynamic range and the high complexity of the molecules of interest. In LC-MS experiments, the inconsistent variation in the travel time of analytes in the LC column results in nonlinear shifts in the LC retention time (RT). This variability must be corrected to accurately match corresponding peptide features across samples in LC-MS experiments. Standard methods for RT alignment applied to the raw data are computationally expensive, making it impractical to process a large number of samples. More successful algorithms perform the alignment on features that matched across experiments based on pre-specified mass and RT windows. Features that match across multiple experiments are more likely to be true positives and, therefore, will be more suitable to drive the alignment correction. However, depending on the feature matching algorithm, ambiguities can arise when more than one candidate feature match falls within the specified windows which might affect the alignment performance. In addition, some of the feature-based alignment algorithms do not correct for nonlinear RT shifts. We propose a novel feature matching algorithm that incorporates wavelet-based shape information about the features. We tested our algorithm on two different applications of MS. First, we combined the feature matching algorithm with a robust nonparametric kernel-type regression to form a nonlinear feature-based alignment framework for LC-MS experiments. We validated our alignment framework on LC-MS data from complex samples with known spiked-in proteins, demonstrating our ability to correctly identify each of them with higher reproducibility and probability score when comparing with the SuperHirn software. In addition, by using our feature-based alignment framework, we were able to increase the number of matched features and improve the correlation between replicates. Second, we tested our feature matching algorithm on MALDI MS with MS/MS acquisitions. We found that using only features that matched across replicates of tandem mass spectra we could improve the identification of peptides compared with the current state-of-the-art software. Supplementary Material is available online at www.libertonline.com/cmb .

Resumo Limpo

character protein via liquid chromatographymass spectrometri lcms tandem ms challeng due larg dynam rang high complex molecul interest lcms experi inconsist variat travel time analyt lc column result nonlinear shift lc retent time rt variabl must correct accur match correspond peptid featur across sampl lcms experi standard method rt align appli raw data comput expens make impract process larg number sampl success algorithm perform align featur match across experi base prespecifi mass rt window featur match across multipl experi like true posit therefor will suitabl drive align correct howev depend featur match algorithm ambigu can aris one candid featur match fall within specifi window might affect align perform addit featurebas align algorithm correct nonlinear rt shift propos novel featur match algorithm incorpor waveletbas shape inform featur test algorithm two differ applic ms first combin featur match algorithm robust nonparametr kerneltyp regress form nonlinear featurebas align framework lcms experi valid align framework lcms data complex sampl known spikedin protein demonstr abil correct identifi higher reproduc probabl score compar superhirn softwar addit use featurebas align framework abl increas number match featur improv correl replic second test featur match algorithm maldi ms msms acquisit found use featur match across replic tandem mass spectra improv identif peptid compar current stateoftheart softwar supplementari materi avail onlin wwwlibertonlinecomcmb

Resumos Similares

IEEE Trans Pattern Anal Mach Intell - Multi-View Face Detection and Registration Requiring Minimal Manual Intervention. ( 0,780000526727763 )
Comput. Biol. Med. - A bilateral analysis scheme for false positive reduction in mammogram mass detection. ( 0,726700257070261 )
IEEE Trans Image Process - Establishing point correspondence of 3D faces via sparse facial deformable model. ( 0,711592213221106 )
IEEE Trans Image Process - Accurate moving cast shadow suppression based on local color constancy detection. ( 0,681494491318408 )
IEEE Trans Image Process - A new multivariate statistical model for change detection in images acquired by homogeneous and heterogeneous sensors. ( 0,678050897536653 )
IEEE Trans Image Process - Weighted color and texture sample selection for image matting. ( 0,657795140609423 )
IEEE Trans Pattern Anal Mach Intell - Handwritten Chinese/Japanese Text Recognition Using Semi-Markov Conditional Random Fields. ( 0,648250352107795 )
IEEE Trans Image Process - Flip-invariant SIFT for copy and object detection. ( 0,642377151140064 )
IEEE J Biomed Health Inform - A new tongue colorchecker design by space representation for precise correction. ( 0,634371508212291 )
IEEE Trans Vis Comput Graph - SuperMatching: Feature Matching Using Supersymmetric Geometric Constraints. ( 0,626744186046512 )
Comput Methods Programs Biomed - Texture and moments-based classification of the acrosome integrity of boar spermatozoa images. ( 0,626473546059658 )
IEEE Trans Image Process - Edge-SIFT: discriminative binary descriptor for scalable partial-duplicate mobile search. ( 0,622218524330007 )
IEEE Trans Image Process - Local directional number pattern for face analysis: face and expression recognition. ( 0,615710532074803 )
IEEE Trans Image Process - Extracting dominant textures in real time with multi-scale hue-saturation-intensity histograms. ( 0,607979744978003 )
Methods Inf Med - A simplification and implementation of random-effects meta-analyses based on the exact distribution of Cochran's Q. ( 0,607431713442464 )
IEEE Trans Image Process - Learning templates for artistic portrait lighting analysis. ( 0,606989680958783 )
IEEE Trans Pattern Anal Mach Intell - Pose-Robust Recognition of Low-Resolution Face Images. ( 0,604702206022532 )
IEEE Trans Image Process - Extracting multiple features in the CID color space for face recognition. ( 0,599116491457131 )
J Biomed Inform - Controlling false match rates in record linkage using extreme value theory. ( 0,59911213283029 )
IEEE Trans Image Process - USB: ultrashort binary descriptor for fast visual matching and retrieval. ( 0,598619756317381 )
IEEE Trans Image Process - Sparse color interest points for image retrieval and object categorization. ( 0,596517828985517 )
Int J Comput Assist Radiol Surg - Fully automatic segmentation of the femur from 3D-CT images using primitive shape recognition and statistical shape models. ( 0,595327481295266 )
IEEE Trans Image Process - PDE-based enhancement of color images in RGB space. ( 0,592786188742392 )
IEEE Trans Pattern Anal Mach Intell - Learning Hybrid Image Templates (HIT) by Information Projection. ( 0,590953992323646 )
IEEE Trans Image Process - On optimal dynamic sequential search for matching in real-time machine vision. ( 0,589545733511533 )
IEEE Trans Image Process - Robust weighted graph transformation matching for rigid and nonrigid image registration. ( 0,589382356688381 )
Artif Intell Med - Scattering features for lung cancer detection in fibered confocal fluorescence microscopy images. ( 0,587819897944839 )
IEEE Trans Vis Comput Graph - Learning Optimized Local Difference Binaries for Scalable Augmented Reality on Mobile Devices. ( 0,587677028287968 )
IEEE Trans Image Process - Robust face representation using hybrid spatial feature interdependence matrix. ( 0,587062650203216 )
IEEE Trans Pattern Anal Mach Intell - A Markov Random Field Groupwise Registration Framework for Face Recognition. ( 0,585885086274824 )
IEEE Trans Image Process - Common feature discriminant analysis for matching infrared face images to optical face images. ( 0,582876021519974 )
IEEE Trans Image Process - HSOG: a novel local image descriptor based on histograms of the second-order gradients. ( 0,582012758101987 )
IEEE Trans Image Process - Random phase textures: theory and synthesis. ( 0,580329691967526 )
IEEE Trans Image Process - Robust pairwise matching of interest points with complex wavelets. ( 0,578829060127706 )
J Med Syst - Comparison of several texture features for tumor detection in CE images. ( 0,577010810507653 )
IEEE Trans Image Process - Face recognition system using multiple face model of hybrid Fourier feature under uncontrolled illumination variation. ( 0,577009144201575 )
IEEE Trans Image Process - Fusing local patterns of Gabor magnitude and phase for face recognition. ( 0,572583161530612 )
IEEE Trans Image Process - Shape vocabulary: a robust and efficient shape representation for shape matching. ( 0,572171953430941 )
IEEE Trans Image Process - Face recognition by exploring information jointly in space, scale and orientation. ( 0,57062508458381 )
IEEE Trans Image Process - Multi-illuminant estimation with conditional random fields. ( 0,570439407580937 )
Artif Intell Med - A decision support system for Crithidia luciliae image classification. ( 0,570190558770384 )
IEEE Trans Vis Comput Graph - Content-Aware Photo Collage Using Circle Packing. ( 0,569854234445947 )
IEEE Trans Image Process - Subspace-based discrete transform encoded local binary patterns representations for robust periocular matching on NIST's face recognition grand challenge. ( 0,569816189103765 )
IEEE Trans Image Process - Normalization of face illumination based on large-and small-scale features. ( 0,569347878111285 )
IEEE Trans Image Process - Enhanced local texture feature sets for face recognition under difficult lighting conditions. ( 0,568100430291345 )
IEEE Trans Image Process - Scale- and rotation-invariant local binary pattern using scale-adaptive texton and subuniform-based circular shift. ( 0,567501545296595 )
IEEE Trans Image Process - Automatic virus particle selection--the entropy approach. ( 0,567124462354392 )
IEEE Trans Image Process - Coupled binary embedding for large-scale image retrieval. ( 0,566884589152577 )
IEEE Trans Pattern Anal Mach Intell - Local Pyramidal Descriptors for Image Recognition. ( 0,56499995272714 )
Int J Comput Assist Radiol Surg - Automated quality assessment of retinal fundus photos. ( 0,563088303968727 )
Comput. Biol. Med. - A correlation analysis-based detection and delineation of ECG characteristic events using template waveforms extracted by ensemble averaging of clustered heart cycles. ( 0,562460679654794 )
IEEE Trans Pattern Anal Mach Intell - Learning Discriminant Face Descriptor. ( 0,562002406814592 )
IEEE Trans Image Process - Nonrigid brain MR image registration using uniform spherical region descriptor. ( 0,56077074477791 )
IEEE Trans Image Process - Scale-invariant features and polar descriptors in omnidirectional imaging. ( 0,558646187010107 )
IEEE Trans Neural Netw Learn Syst - Incremental Generalized Discriminative Common Vectors for Image Classification. ( 0,557565172519322 )
IEEE Trans Image Process - A Unified Methodology for Computing Accurate Quaternion Color Moments and Moment Invariants. ( 0,556760843107683 )
J Med Syst - A new Watermarking System based on Discrete Cosine Transform (DCT) in color biometric images. ( 0,555590588640777 )
IEEE J Biomed Health Inform - Thermal imaging as a biometrics approach to facial signature authentication. ( 0,555040240816676 )
IEEE Trans Image Process - Color local texture features for color face recognition. ( 0,554740930840728 )
IEEE Trans Image Process - Combining LBP difference and feature correlation for texture description. ( 0,554677216417795 )
IEEE Trans Image Process - A novel local pattern descriptor--local vector pattern in high-order derivative space for face recognition. ( 0,553549792007672 )
IEEE Trans Image Process - Discovering discriminative graphlets for aerial image categories recognition. ( 0,552832033459272 )
IEEE Trans Image Process - Color constancy by category correlation. ( 0,551825980053866 )
IEEE Trans Image Process - Missing texture reconstruction method based on error reduction algorithm using Fourier transform magnitude estimation scheme. ( 0,551440768100787 )
IEEE Trans Image Process - Global propagation of affine invariant features for robust matching. ( 0,551218588428269 )
IEEE Trans Pattern Anal Mach Intell - Scalable Face Image Retrieval with Identity-Based Quantization and Multireference Reranking. ( 0,55102795931696 )
IEEE Trans Image Process - Local energy pattern for texture classification using self-adaptive quantization thresholds. ( 0,550907135784464 )
IEEE Trans Image Process - Wavelet modeling using finite mixtures of generalized gaussian distributions: application to texture discrimination and retrieval. ( 0,550381069662279 )
Int J Neural Syst - Retrieval of noisy fingerprint patterns using metric attractor networks. ( 0,549893486098454 )
IEEE Trans Image Process - Scale-invariant features for 3-D mesh models. ( 0,549670629038277 )
Int J Med Robot - Robotic system with sweeping palpation and needle biopsy for prostate cancer diagnosis. ( 0,54889956640447 )
IEEE Trans Image Process - Wavelet domain multifractal analysis for static and dynamic texture classification. ( 0,548860481016796 )
IEEE Trans Image Process - A probabilistic approach for color correction in image mosaicking applications. ( 0,548663622582297 )
IEEE Trans Image Process - Object segmentation of database images by dual multiscale morphological reconstructions and retrieval applications. ( 0,547462910833885 )
IEEE Trans Image Process - A feature-based learning framework for accurate prostate localization in CT images. ( 0,546831070836994 )
IEEE Trans Image Process - Generalized random walks for fusion of multi-exposure images. ( 0,546323842137362 )
Med Biol Eng Comput - Object-shape recognition and 3D reconstruction from tactile sensor images. ( 0,545971731528832 )
Comput Math Methods Med - Extraction of prostatic lumina and automated recognition for prostatic calculus image using PCA-SVM. ( 0,545827633378933 )
Comput Math Methods Med - Membership-degree preserving discriminant analysis with applications to face recognition. ( 0,545670193030865 )
Neural Comput - Nonparametric estimation of K?llback-Leibler divergence. ( 0,545544725589981 )
Int J Neural Syst - Low-rank approximation based non-negative multi-way array decomposition on event-related potentials. ( 0,544879028826017 )
Comput. Biol. Med. - Melanomas non-invasive diagnosis application based on the ABCD rule and pattern recognition image processing algorithms. ( 0,544612439809605 )
IEEE Trans Pattern Anal Mach Intell - Intensity-Based Image Registration by Nonparametric Local Smoothing. ( 0,544574631134311 )
Comput Biol Chem - Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment. ( 0,543005962040125 )
IEEE Trans Image Process - Pose-invariant face recognition using Markov random fields. ( 0,542132111212336 )
Comput Methods Programs Biomed - Conditional mutual information-based feature selection for congestive heart failure recognition using heart rate variability. ( 0,542091559425808 )
Methods Inf Med - The utility of imputed matched sets. Analyzing probabilistically linked databases in a low information setting. ( 0,540252952263489 )
IEEE Trans Image Process - Semantic pyramids for gender and action recognition. ( 0,539959101943029 )
IEEE Trans Pattern Anal Mach Intell - LDAHash: Improved Matching with Smaller Descriptors. ( 0,539916161903619 )
IEEE Trans Image Process - Region merging techniques using information theory statistical measures. ( 0,539775439919963 )
IEEE Trans Image Process - A uniform grid structure to speed up example-based photometric stereo. ( 0,539560549104476 )
IEEE Trans Image Process - A completed modeling of local binary pattern operator for texture classification. ( 0,538216319875881 )
IEEE Trans Image Process - Local color vector binary patterns from multichannel face images for face recognition. ( 0,537544422577253 )
IEEE Trans Image Process - Color constancy using 3D scene geometry derived from a single image. ( 0,537102008088684 )
Int J Comput Assist Radiol Surg - An evaluation of image descriptors combined with clinical data for breast cancer diagnosis. ( 0,537053466901864 )
Med Biol Eng Comput - Noninvasive and automatic diagnosis of patients at high risk of swallowing aspiration. ( 0,53584247911612 )
Comput Math Methods Med - Computer aided quantification of pathological features for flexor tendon pulleys on microscopic images. ( 0,53531214208096 )
IEEE Trans Image Process - Principal visual word discovery for automatic license plate detection. ( 0,534408551673238 )
IEEE Trans Pattern Anal Mach Intell - Segmentation, Inference and Classification of Partially Overlapping Nanoparticles. ( 0,534009764918186 )
IEEE Trans Image Process - An attribute-assisted reranking model for web image search. ( 0,5337308771793 )