Regular Article
Improved peak detection and quantification of mass spectrometry data acquired from surface‐enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform
Abstract
Mass spectrometry is being used to find disease‐related patterns in mixtures of proteins derived from biological fluids. Questions have been raised about the reproducibility and reliability of peak quantifications using this technology. We collected nipple aspirate fluid from breast cancer patients and healthy women, pooled them into a quality control sample, and produced 24 replicate SELDI spectra. We developed a novel algorithm to process the spectra, denoising with the undecimated discrete wavelet transform (UDWT), and evaluated it for consistency and reproducibility. UDWT efficiently decomposes spectra into noise and signal. The noise is consistent and uncorrelated. Baseline correction produces isolated peak clusters separated by flat regions. Our method reproducibly detects more peaks than the method implemented in Ciphergen software. After normalization and log transformation, the mean coefficient of variation of peak heights is 10.6%. Our method to process spectra provides improvements over existing methods. Denoising using the UDWT appears to be an important step toward obtaining results that are more accurate. It improves the reproducibility of quantifications and supplies tools for investigation of the variations in the technology more carefully. Further study will be required, because we do not have a gold standard providing an objective assessment of which peaks are present in the samples.
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Number of times cited according to CrossRef: 190
- Swati Bhardwaj, Venkateshwarlu Yellaswamy Gudur, Amit Acharyya, An Accelerated Computational Approach in Proteomics, Biomedical Signal Processing, 10.1007/978-981-13-9097-5_16, (389-432), (2020).
- Tijmen S. Bos, Wouter C. Knol, Stef R.A. Molenaar, Leon E. Niezen, Peter J. Schoenmakers, Govert W. Somsen, Bob W.J. Pirok, Recent applications of chemometrics in one‐ and two‐dimensional chromatography, Journal of Separation Science, 10.1002/jssc.202000011, 43, 9-10, (1678-1727), (2020).
- Florian Lieb, Tobias Boskamp, Hans-Georg Stark, Peak detection for MALDI mass spectrometry imaging data using sparse frame multipliers, Journal of Proteomics, 10.1016/j.jprot.2020.103852, 225, (103852), (2020).
- Nico Verbeeck, Richard M. Caprioli, Raf Van de Plas, Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry, Mass Spectrometry Reviews, 10.1002/mas.21602, 39, 3, (245-291), (2019).
- Scott Loranger, Geir Pedersen, Thomas C. Weber, Broadband acoustic scattering from oblate hydrocarbon droplets, The Journal of the Acoustical Society of America, 10.1121/1.5121699, 146, 2, (1176-1188), (2019).
- Jun Li, Yuanlu Li, Weijing Zhao, Min Jiang, Diffusion enhancement model and its application in peak detection, Chemometrics and Intelligent Laboratory Systems, 10.1016/j.chemolab.2019.04.012, (2019).
- Vincent Picaud, Jean-Francois Giovannelli, Caroline Truntzer, Jean-Philippe Charrier, Audrey Giremus, Pierre Grangeat, Catherine Mercier, Linear MALDI-ToF simultaneous spectrum deconvolution and baseline removal, BMC Bioinformatics, 10.1186/s12859-018-2116-3, 19, 1, (2018).
- M. Smitha, A. K. Nisa, K. Archana, Diabetic Retinopathy Detection in Fundus Image Using Cross Sectional Profiles and ANN, Computational Vision and Bio Inspired Computing, 10.1007/978-3-319-71767-8_84, (982-993), (2018).
- Yuanlu Li, Fawang Liu, Ian W. Turner, Tao Li, Time-fractional diffusion equation for signal smoothing, Applied Mathematics and Computation, 10.1016/j.amc.2018.01.007, 326, (108-116), (2018).
- Yuanlu Li, Min Jiang, Fawang Liu, Time fractional super-diffusion model and its application in peak-preserving smoothing, Chemometrics and Intelligent Laboratory Systems, 10.1016/j.chemolab.2018.02.005, 175, (13-19), (2018).
- Mohamad Sabri bin SINAL, Eiji KAMIOKA, Hybrid Mechanism to Detect Paroxysmal Stage of Atrial Fibrillation Using Adaptive Threshold-Based Algorithm with Artificial Neural Network, IEICE Transactions on Information and Systems, 10.1587/transinf.2017EDP7235, E101.D, 6, (1666-1676), (2018).
- Seok-Beom Roh, Sung-Kwun Oh, Witold Pedrycz, Identification of Black Plastics Based on Fuzzy RBF Neural Networks: Focused on Data Preprocessing Techniques Through Fourier Transform Infrared Radiation, IEEE Transactions on Industrial Informatics, 10.1109/TII.2017.2771254, 14, 5, (1802-1813), (2018).
- Javier Palarea-Albaladejo, Kevin Mclean, Frank Wright, David G E Smith, MALDIrppa: quality control and robust analysis for mass spectrometry data, Bioinformatics, 10.1093/bioinformatics/btx628, 34, 3, (522-523), (2017).
- Michal Marczyk, Joanna Polanska, Andrzej Polanski, undefined, 2017 3rd International Conference on Frontiers of Signal Processing (ICFSP), 10.1109/ICFSP.2017.8097057, (39-43), (2017).
- Jochen Kruppa, Klaus Jung, Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots, BMC Bioinformatics, 10.1186/s12859-017-1645-5, 18, 1, (2017).
- Woohyun Kim, Srinivas Katipamula, Robert Lutes, Improving HVAC operational efficiency in small-and medium-size commercial buildings, Building and Environment, 10.1016/j.buildenv.2017.05.010, 120, (64-76), (2017).
- Paolo Inglese, James S. McKenzie, Anna Mroz, James Kinross, Kirill Veselkov, Elaine Holmes, Zoltan Takats, Jeremy K. Nicholson, Robert C. Glen, Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer, Chemical Science, 10.1039/C6SC03738K, 8, 5, (3500-3511), (2017).
- Jeffrey S. Morris, Veerabhadran Baladandayuthapani, Statistical contributions to bioinformatics: Design, modelling, structure learning and integration, Statistical Modelling: An International Journal, 10.1177/1471082X17698255, 17, 4-5, (245-289), (2017).
- Rim Ghozzi, Samer Lahouar, Chokri Souani, Kamel Besbes, undefined, 2017 International Conference on Advanced Systems and Electric Technologies (IC_ASET), 10.1109/ASET.2017.7983663, (34-37), (2017).
- Sebastian Gibb, Korbinian Strimmer, Mass Spectrometry Analysis Using MALDIquant, Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry, 10.1007/978-3-319-45809-0, (101-124), (2017).
- Bart J. A. Mertens, Logistic Regression Modeling on Mass Spectrometry Data in Proteomics Case-Control Discriminant Studies, Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry, 10.1007/978-3-319-45809-0, (213-238), (2017).
- Kishore Kumar Jagadeesan, Simon Ekström, MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis, SLAS DISCOVERY: Advancing Life Sciences R&D, 10.1177/2472555217727517, 22, 10, (1246-1252), (2017).
- Christine Laronga, Richard R. Drake, Proteomic Approach to Breast Cancer, Cancer Control, 10.1177/107327480701400406, 14, 4, (360-368), (2017).
- Hyunjin Shin, Miray Mutlu, John M. Koomen, Mia K. Markey, Parametric Power Spectral Density Analysis of Noise from Instrumentation in MALDI TOF Mass Spectrometry, Cancer Informatics, 10.1177/117693510700300019, 3, (117693510700300), (2017).
- Changyu Shen, Timothy E Breen, Lacey E Dobrolecki, C. Max Schmidt, George W. Sledge, Kathy D. Miller, Robert J Hickey, Comparison of Computational Algorithms for the Classification of Liver Cancer using SELDI Mass Spectrometry: A Case Study, Cancer Informatics, 10.1177/117693510700300021, 3, (117693510700300), (2017).
- Constantin F. Aliferis, Alexander Statnikov, Ioannis Tsamardinos, Challenges in the Analysis of Mass-Throughput Data: A Technical Commentary from the Statistical Machine Learning Perspective, Cancer Informatics, 10.1177/117693510600200004, 2, (117693510600200), (2017).
- Jialiang Li, Qunqiang Feng, Jason P Fine, Michael J Pencina, Ben Van Calster, Nonparametric estimation and inference for polytomous discrimination index, Statistical Methods in Medical Research, 10.1177/0962280217692830, (096228021769283), (2017).
- Yuanlu Li, Min Jiang, Spatial-fractional order diffusion filtering, Journal of Mathematical Chemistry, 10.1007/s10910-017-0795-z, (2017).
- Y. Melodie Du, Ye Hu, Yu Xia, Zheng Ouyang, Power Normalization for Mass Spectrometry Data Analysis and Analytical Method Assessment, Analytical Chemistry, 10.1021/acs.analchem.5b04418, 88, 6, (3156-3163), (2016).
- Tsung-Heng Tsai, Minkun Wang, Habtom W. Ressom, Preprocessing and Analysis of LC-MS-Based Proteomic Data, Statistical Analysis in Proteomics, 10.1007/978-1-4939-3106-4_3, (63-76), (2016).
- Yuanlu Li, Yaqing Ding, Tiao Li, Nonlinear diffusion filtering for peak-preserving smoothing of a spectrum signal, Chemometrics and Intelligent Laboratory Systems, 10.1016/j.chemolab.2016.06.007, 156, (157-165), (2016).
- Xia Tong, Zhimin Zhang, Fanjuan Zeng, Chunyan Fu, Pan Ma, Ying Peng, Hongmei Lu, Yizeng Liang, Recursive Wavelet Peak Detection of Analytical Signals, Chromatographia, 10.1007/s10337-016-3155-4, 79, 19-20, (1247-1255), (2016).
- Xianlin Han, Quantification of Individual Lipid Species in Lipidomics, Lipidomics, 10.1002/9781119085263, (305-334), (2016).
- Younghoon Kim, Kevin A. Schug, Seoung Bum Kim, An ensemble regularization method for feature selection in mass spectral fingerprints, Chemometrics and Intelligent Laboratory Systems, 10.1016/j.chemolab.2015.05.009, 146, (322-328), (2015).
- Chalini D Wijetunge, Isaam Saeed, Berin A Boughton, Ute Roessner, Saman K Halgamuge, A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model, BMC Genomics, 10.1186/1471-2164-16-S12-S12, 16, S12, (2015).
- Zhi-Min Zhang, Xia Tong, Ying Peng, Pan Ma, Ming-Jin Zhang, Hong-Mei Lu, Xiao-Qing Chen, Yi-Zeng Liang, Multiscale peak detection in wavelet space, The Analyst, 10.1039/C5AN01816A, 140, 23, (7955-7964), (2015).
- Mst. Papia Sultana and Jialiang Li, Jianhua Hu, Comparison of three‐dimensional ROC surfaces for clustered and correlated markers, with a proteomics application, Statistica Neerlandica, 10.1111/stan.12065, 69, 4, (399-418), (2015).
- Andrew Palmer, Ekaterina Ovchinnikova, Mikael Thuné, Régis Lavigne, Blandine Guével, Andrey Dyatlov, Olga Vitek, Charles Pineau, Mats Borén, Theodore Alexandrov, Using collective expert judgements to evaluate quality measures of mass spectrometry images, Bioinformatics, 10.1093/bioinformatics/btv266, 31, 12, (i375-i384), (2015).
- Zaw Zaw Htike, Shoon Lei Win, Premalignant Pancreatic Cancer Diagnosis Using Proteomic Pattern Analysis, Journal of Medical and Bioengineering, 10.12720/jomb.4.4.288-292, 4, 4, (288-292), (2015).
- H. López-Fernández, H. M. Santos, J. L. Capelo, F. Fdez-Riverola, D. Glez-Peña, M. Reboiro-Jato, Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery, BMC Bioinformatics, 10.1186/s12859-015-0752-4, 16, 1, (2015).
- Sara Nasso, Sandra Goetze, Lennart Martens, Ariadne’s Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data, Journal of Proteome Research, 10.1021/pr500996s, 14, 9, (3779-3792), (2015).
- Gautam Bhattacharya, Koushik Ghosh, Ananda S. Chowdhury, Outlier detection using neighborhood rank difference, Pattern Recognition Letters, 10.1016/j.patrec.2015.04.004, 60-61, (24-31), (2015).
- Selvaraaju Murugesan, David B.H. Tay, Ira Cooke, Pierre Faou, Application of dual tree complex wavelet transform in tandem mass spectrometry, Computers in Biology and Medicine, 10.1016/j.compbiomed.2015.05.002, 63, (36-41), (2015).
- Yuanjie Liu, Xiaoguang Zhou, Yude Yu, A concise iterative method using the Bezier technique for baseline construction, The Analyst, 10.1039/C5AN01184A, 140, 23, (7984-7996), (2015).
- Sheng Ren, Anna A. Hinzman, Emily L. Kang, Rhonda D. Szczesniak, Long Jason Lu, Computational and statistical analysis of metabolomics data, Metabolomics, 10.1007/s11306-015-0823-6, 11, 6, (1492-1513), (2015).
- Tonio Oumeraci, Vanessa Jensen, Steven R. Talbot, Winfried Hofmann, Markus Kostrzewa, Brigitte Schlegelberger, Nils von Neuhoff, Susanne Häussler, Comprehensive MALDI-TOF Biotyping of the Non-Redundant Harvard Pseudomonas aeruginosa PA14 Transposon Insertion Mutant Library, PLOS ONE, 10.1371/journal.pone.0117144, 10, 2, (e0117144), (2015).
- Andrzej Polanski, Michal Marczyk, Monika Pietrowska, Piotr Widlak, Joanna Polanska, Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry, PLOS ONE, 10.1371/journal.pone.0134256, 10, 7, (e0134256), (2015).
- Matthias Schwartz, Björn Meyer, Bernhard Wirnitzer, Carsten Hopf, Standardized processing of MALDI imaging raw data for enhancement of weak analyte signals in mouse models of gastric cancer and Alzheimer’s disease, Analytical and Bioanalytical Chemistry, 10.1007/s00216-014-8356-9, 407, 8, (2255-2264), (2014).
- S. Shanmugam, P. SrinivasaPerumal, Spectral matching approaches in hyperspectral image processing, International Journal of Remote Sensing, 10.1080/01431161.2014.980922, 35, 24, (8217-8251), (2014).
- Caroline Truntzer, Elise Mostacci, Aline Jeannin, Jean-Michel Petit, Patrick Ducoroy, Hervé Cardot, Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data, BMC Bioinformatics, 10.1186/s12859-014-0385-z, 15, 1, (2014).
- Anthony J. Kearsley, Yutheeka Gadhyan, William E. Wallace, Stochastic regression modeling of chemical spectra, Chemometrics and Intelligent Laboratory Systems, 10.1016/j.chemolab.2014.08.002, 139, (26-32), (2014).
- Guangxu Jin, Stephen T.C. Wong, Proteomics-Based Theranostics, Cancer Theranostics, 10.1016/B978-0-12-407722-5.00003-7, (21-42), (2014).
- Ros Surya Taher, Nursuriati Jamil, Sharifalillah Nordin, Umikalsum Mohamed Bahari, undefined, 2014 14th International Conference on Intelligent Systems Design and Applications, 10.1109/ISDA.2014.7066267, (180-186), (2014).
- Tom J. Zajdel, Michaela A. TerAvest, Behzad Rad, Caroline M. Ajo-Franklin, Michel M. Maharbiz, undefined, IEEE SENSORS 2014 Proceedings, 10.1109/ICSENS.2014.6985366, (1764-1767), (2014).
- Rahul Biswas, Koulik Khamaru, Kaushik K. Majumdar, A Peak Synchronization Measure for Multiple Signals, IEEE Transactions on Signal Processing, 10.1109/TSP.2014.2333568, 62, 17, (4390-4398), (2014).
- Joseph P Salisbury, Qian Liu, Jeffrey N Agar, QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure, BMC Bioinformatics, 10.1186/s12859-014-0403-1, 15, 1, (2014).
- Andrea Jurisicova, Igor Jurisica, Thomas Kislinger, Advances in ovarian cancer proteomics: the quest for biomarkers and improved therapeutic interventions, Expert Review of Proteomics, 10.1586/14789450.5.4.551, 5, 4, (551-560), (2014).
- Howard B Gutstein, Jeffrey S Morris, Laser capture sampling and analytical issues in proteomics, Expert Review of Proteomics, 10.1586/14789450.4.5.627, 4, 5, (627-637), (2014).
- Abdelali Haoudi, Halima Bensmail, Bioinformatics and data mining in proteomics, Expert Review of Proteomics, 10.1586/14789450.3.3.333, 3, 3, (333-343), (2014).
- Kenji Nakayama, Takahiro Inoue, Sadanori Sekiya, Naoki Terada, Yu Miyazaki, Takayuki Goto, Shigeki Kajihara, Shin-Ichiro Kawabata, Shinichi Iwamoto, Kuniko Ikawa, Junko Oosaga, Hiroaki Tsuji, Koichi Tanaka, Osamu Ogawa, The C-Terminal Fragment of Prostate-Specific Antigen, a 2331 Da Peptide, as a New Urinary Pathognomonic Biomarker Candidate for Diagnosing Prostate Cancer, PLoS ONE, 10.1371/journal.pone.0107234, 9, 9, (e107234), (2014).
- Miguel García-Torres, Rubén Armañanzas, Concha Bielza, Pedro Larrañaga, Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data, Information Sciences, 10.1016/j.ins.2010.12.013, 222, (229-246), (2013).
- Mavuduru Neehar, Amit Acharyya, undefined, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 10.1109/EMBC.2013.6610095, (2692-2695), (2013).
- Syarifah Adilah Mohamed Yusoff, Rosni Abdullah, Ibrahim Venkat, Using ABC Algorithm with Shrinkage Estimator to Identify Biomarkers of Ovarian Cancer from Mass Spectrometry Analysis, Hybrid Artificial Intelligent Systems, 10.1007/978-3-642-40846-5_35, (345-355), (2013).
- Susmita Datta, Feature Selection and Machine Learning with Mass Spectrometry Data, Mass Spectrometry Data Analysis in Proteomics, 10.1007/978-1-62703-392-3_10, (237-262), (2013).
- Istvan Lazar, Andras Hajdu, Retinal Microaneurysm Detection Through Local Rotating Cross-Section Profile Analysis, IEEE Transactions on Medical Imaging, 10.1109/TMI.2012.2228665, 32, 2, (400-407), (2013).
- Joseph P Salisbury, Kristin J Boggio, Yun-Wei A Hsu, Jeniffer Quijada, Anna Sivachenko, Gabriele Gloeckner, Paul J Kowalski, Michael L Easterling, Michael Rosbash, Jeffrey N Agar, A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics, Molecular Brain, 10.1186/1756-6606-6-60, 6, 1, (60), (2013).
- S. Amir, undefined Haihui Wang, undefined Fangtao Sun, undefined, Proceedings of 2013 10th International Bhurban Conference on Applied Sciences & Technology (IBCAST), 10.1109/IBCAST.2013.6512140, (109-112), (2013).
- Zengyou He, Robert Z. Qi, Weichuan Yu, Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery, Applications of MALDI-TOF Spectroscopy, 10.1007/128_2012_365, (193-209), (2013).
- Alexander A. Aksenov, Ana V. Guaman Novillo, Sindhuja Sankaran, Alexander G. Fung, Alberto Pasamontes, Frederico Martinelli, William H. K. Cheung, Reza Ehsani, Abhaya M. Dandekar, Cristina E. Davis, Volatile Organic Compounds (VOCs) for Noninvasive Plant Diagnostics, Pest Management with Natural Products, 10.1021/bk-2013-1141.ch006, (73-95), (2013).
- Bin Zhu, David B. Dunson, Locally Adaptive Bayes Nonparametric Regression via Nested Gaussian Processes, Journal of the American Statistical Association, 10.1080/01621459.2013.838568, 108, 504, (1445-1456), (2013).
- Penghao Wang, Albert Y. Zomaya, Cleansing of Mass Spectrometry Data for Protein Identification and Quantification, Biological Knowledge Discovery Handbook, 10.1002/9781118617151, (59-76), (2013).
- Julia Wattacheril, Erin H. Seeley, Peggi Angel, Heidi Chen, Benjamin P. Bowen, Christian Lanciault, Richard M.Caprioli, Naji Abumrad, Charles Robb Flynn, Differential Intrahepatic Phospholipid Zonation in Simple Steatosis and Nonalcoholic Steatohepatitis, PLoS ONE, 10.1371/journal.pone.0057165, 8, 2, (e57165), (2013).
- Jens Fiala, Philipp Bingger, Dominic Ruh, Katharina Foerster, Claudia Heilmann, Friedhelm Beyersdorf, Hans Zappe, Andreas Seifert, An implantable optical blood pressure sensor based on pulse transit time, Biomedical Microdevices, 10.1007/s10544-012-9689-9, 15, 1, (73-81), (2012).
- M. Y. SyarifahAdilah, Rosni Abdullah, Ibrahim Venkat, undefined, 2012 4th Conference on Data Mining and Optimization (DMO), 10.1109/DMO.2012.6329800, (67-72), (2012).
- undefined Wei Hu, undefined Xingguo Yang, undefined Fugang Xu, undefined Minghui Hao, undefined, 2012 2nd International Conference on Uncertainty Reasoning and Knowledge Engineering, 10.1109/URKE.2012.6319562, (264-267), (2012).
- Szu-Wei Chou, Guo-Rung Shiu, Huan-Cheng Chang, Wen-Ping Peng, Wavelet-Based Method for Time-Domain Noise Analysis and Reduction in a Frequency-Scan Ion Trap Mass Spectrometer, Journal of The American Society for Mass Spectrometry, 10.1007/s13361-012-0455-2, 23, 11, (1855-1864), (2012).
- Xin Zhang, Dennis E. Shasha, Yang Song, Jason T. L. Wang, Fast Elastic Peak Detection for Mass Spectrometry Data Mining, IEEE Transactions on Knowledge and Data Engineering, 10.1109/TKDE.2010.238, 24, 4, (634-648), (2012).
- undefined Chao Yang, undefined Zengyou He, undefined Can Yang, undefined Weichuan Yu, Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2012.29, 9, 4, (1212-1219), (2012).
- Marco Chierici, Davide Albanese, Pietro Franceschi, Cesare Furlanello, TOFwave: reproducibility in biomarker discovery from time-of-flight mass spectrometry data, Molecular BioSystems, 10.1039/c2mb25223f, 8, 11, (2845), (2012).
- Jinhai Liu, Zhibo Yu, A Filtering Method for Pressure Time Series of Oil Pipelines, Advances in Brain Inspired Cognitive Systems, 10.1007/978-3-642-31561-9_21, (192-197), (2012).
- Lin Ji, Gitanjali Jayachandran, Jack A. Roth, High Throughput Profiling of Serum Phosphoproteins/Peptides Using the SELDI-TOF-MS Platform, SELDI-TOF Mass Spectrometry, 10.1007/978-1-61779-418-6_14, (199-216), (2012).
- Jeffrey C. Miecznikowski, Kimberly F. Sellers, William F. Eddy, Multidimensional Median Filters for Finding Bumps in Chemical Sensor Datasets, Journal of Sensor Technology, 10.4236/jst.2012.21005, 02, 01, (23-37), (2012).
- Sébastien Li-Thiao-Té, Benno Schwikowski, Feature Detection with Controlled Error Rates in LC/MS Images, Journal of Computational Biology, 10.1089/cmb.2009.0125, 19, 4, (349-364), (2012).
- Petr Pompach, Kevin B. Chandler, Renny Lan, Nathan Edwards, Radoslav Goldman, Semi-Automated Identification of N-Glycopeptides by Hydrophilic Interaction Chromatography, nano-Reverse-Phase LC–MS/MS, and Glycan Database Search, Journal of Proteome Research, 10.1021/pr201183w, 11, 3, (1728-1740), (2012).
- Guang Xu, Xin Liu, Qing Yan Liu, Yanhong Zhou, Jianjun Li, Improve accuracy and sensibility in glycan structure prediction by matching glycan isotope abundance, Analytica Chimica Acta, 10.1016/j.aca.2012.07.009, 743, (80-89), (2012).
- Y. Melodie Du, Wei Xu, Zheng Ouyang, Self-correlation method for processing random phase signals in Fourier Transform Mass Spectrometry, International Journal of Mass Spectrometry, 10.1016/j.ijms.2012.06.013, 325-327, (73-79), (2012).
- S. Bekesova, O. Kosti, K.B. Chandler, J. Wu, H.L. Madej, K.C. Brown, V. Simonyan, R. Goldman, N-glycans in liver-secreted and immunoglogulin-derived protein fractions, Journal of Proteomics, 10.1016/j.jprot.2012.01.024, 75, 7, (2216-2224), (2012).
- Syarifah Adilah Mohamed Yusoff, Ibrahim Venkat, Umi Kalsom Yusof, Rosni Abdullah, Bio-Inspired Metaheuristic Optimization Algorithms for Biomarker Identification in Mass Spectrometry Analysis, International Journal of Natural Computing Research, 10.4018/jncr.2012040104, 3, 2, (64-85), (2012).
- Vincent A. Emanuele II, Gitika Panicker, Brian M. Gurbaxani, Jin-Mann S. Lin, Elizabeth R. Unger, Sensitive and Specific Peak Detection for SELDI-TOF Mass Spectrometry Using a Wavelet/Neural-Network Based Approach, PLoS ONE, 10.1371/journal.pone.0048103, 7, 11, (e48103), (2012).
- Felix Scholkmann, Jens Boss, Martin Wolf, An Efficient Algorithm for Automatic Peak Detection in Noisy Periodic and Quasi-Periodic Signals, Algorithms, 10.3390/a5040588, 5, 4, (588-603), (2012).
- K. Jung, W. Engelke, M. Knosel, Statistical signal processing methods for intraoral pressure curve analysis in orthodontics, The European Journal of Orthodontics, 10.1093/ejo/cjr039, 34, 4, (437-441), (2011).
- Chris Bauer, Rainer Cramer, Johannes Schuchhardt, Evaluation of Peak-Picking Algorithms for Protein Mass Spectrometry, Data Mining in Proteomics, 10.1007/978-1-60761-987-1_22, (341-352), (2011).
- Chris Bauer, Frank Kleinjung, Celia J Smith, Mark W Towers, Ali Tiss, Alexandra Chadt, Tanja Dreja, Dieter Beule, Hadi Al-Hasani, Knut Reinert, Johannes Schuchhardt, Rainer Cramer, Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset, BMC Bioinformatics, 10.1186/1471-2105-12-140, 12, 1, (2011).
- R Armañanzas, Y Saeys, I Inza, M García-Torres, C Bielza, Y van de Peer, P Larrañaga, Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2010.18, 8, 3, (760-774), (2011).
- Lixia Diao, Charlotte H. Clarke, Kevin R. Coombes, Stanley R. Hamilton, Jack Roth, Li Mao, Bogdan Czerniak, Keith A. Baggerly, Jeffrey S. Morris, Eric T. Fung, Robert C. Bast, Reproducibility of SELDI Spectra across Time and Laboratories, Cancer Informatics, 10.4137/CIN.S6438, 10, (CIN.S6438), (2011).
- Syarifah Adilah M.Y., Ibrahim Venkat, Rosni Abdullah, Umi Kalsom Yusof, undefined, 2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications, 10.1109/BIC-TA.2011.7, (75-79), (2011).
- Karin Noy, Fadi Towfic, Gayle M. Wittenberg, Daniel Fasulo, Shape-Based Feature Matching Improves Protein Identification via LC-MS and Tandem MS, Journal of Computational Biology, 10.1089/cmb.2010.0155, 18, 4, (547-557), (2011).
- Kenji Watanabe, Takumi Kobayashi, Katsuyuki Koike, Tetsuya Higuchi, Tohru Natsume, Nobuyuki Otsu, undefined, 2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 10.1109/ICASSP.2011.5946480, (621-624), (2011).
- Johan de Rooi, Paul Eilers, Deconvolution of pulse trains with the L0 penalty, Analytica Chimica Acta, 10.1016/j.aca.2011.05.030, 705, 1-2, (218-226), (2011).
- Clement S. Sun, Mia K. Markey, Recent advances in computational analysis of mass spectrometry for proteomic profiling, Journal of Mass Spectrometry, 10.1002/jms.1909, 46, 5, (443-456), (2011).
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