| Title |
All Authors |
Session |
Board Number |
| Simulated Srm and Robust Signal Estimates to Aid The Development of Srm Assays for Protein Analytes |
Wen Yu, Leo Bonilla, Mike Davis, Chris Farnsworth, Paul Auger, Kim Lee, Chris Russell, Andy Welcher And Scott Patterson |
A |
1 |
| An Integrated Scoring Algorithm for Improved Characterization of Site-Specific Protein N-Glycolsylations |
Anoop M. Mayampurath, Yin Wu, Zaneer M. Segu, Yehia Mehcref, Haixu Tang |
A |
2 |
| Comparative Proteogenomics |
J Eli Venter, Samuel H Payne |
A |
3 |
| Visual Exploration of Proteogenomic Prokaryotic Data Though The Vespa Platform |
Elena Peterson, Charles Ansong, Hyunjoo Walker, Jeffrey Jensen, Sam Hashemi, Christopher Oehmen, Joshua N. Adkins, and Bobbie-Jo M. Webb-Robertson |
A |
4 |
| Characterization of Histone H2A Variants in Mouse Embryonic Stem Cells Using Quantitative Proteomics and a New Software Tool. |
Hye Ryung Jung, Diego Pasini, Marco Ruijken, Kristian Helin, Ole Nørregaard Jensen |
A |
5 |
| Predicting The Unpredictable: Calculating Retention Time Shifts Associated With Variation of Gradient Slopes in Peptide Rp Hplc |
Vic Spicer, Oleg V. Krokhin |
A |
6 |
| Integrated Bioinformatics Supports The Sequence Characterization of Monoclonal Antibodies Based on a Combined Lc-Ms/Ms Approach |
Jörg Glandorf, Michael Becker, Arndt Asperger, Matthias Witt, Romano Hebeler, Andrea Schneider, Ulrike Schweiger-Hufnagel, Peter Hufnagel |
A |
7 |
| Proteomic Analysis of Centrosome Centromatrix in Spisula Solidissima Using a Novel Search Algorithm |
Shreya Chand, Raphael S. Eidus, Donna E. Crone, Robert E. Palazzo And Mark D. Platt |
A |
8 |
| Machine Learning Approaches to The Assessment of Peptide-Spectrum Matches Without Using a Decoy Database |
Yong Fuga Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang |
A |
9 |
| Quickmod: a Spectral Library Search Tool for Rapid Unsupervised Identification of Modified Peptides in Ms/Ms Data. |
Erik Ahrné, Markus Müller, Yuki Ohta, Frederic Niktin, Frederique Lisacek |
A |
10 |
| Computational Proteomics With a Gene Network in Your Pocket |
Smriti R Ramakrishnan, Edward M Marcotte, Daniel P Miranker |
A |
11 |
| A New Method for Multiple Peak Alignment of Lc-Maldi-Tof Data |
Zhiqun Tang, Lihua Zhang, Amerita K. Cheema, Habtom W. Ressom |
A |
12 |
| Annotation of Prokaryote Genomes Using Large-Scale Proteomic Data |
Hisaaki Taniguchi |
A |
13 |
| Ms/Ms Sequencing of Cyclic Peptides: Revolution or Era? |
Michelle L. Colgrave, Aaron G. Poth, Quentin Kaas, David J. Craik |
A |
14 |
| Charge-State and Sequence-Dependent Scoring Dramatically Improves Matching of Peptide Etd Spectra |
Robert J. Chalkley, Peter R. Baker, Katalin F. Medzihradszky, A. L. Burlingame |
A |
15 |
| Proteoconnections: an Analysis Platform to Accelerate Proteomes and Phosphoproteomes Exploration |
Mathieu Courcelles, Pierre Thibault |
A |
16 |
| Statistical Characterization of Etd Fragmentation Patterns and Its Utilities to Improve Peptide Identification Via Search Engine Pfind 2.1 |
Rui-Xiang Sun, Meng-Qiu Dong, Chun-Qing Song, Hao Chi, Bing Yang, Li-Yun Xiu, Chao Liu, Le-Heng Wang, Yan Fu, And Si-Min He |
A |
17 |
| Developing a Computational Tool for The Automated Large-Scale Gpiomic Analysis |
Clemente Aguilar, Ernesto Nakayasu, Ming-Ying Leung And Igor C. Almeida |
A |
18 |
| Audit: an Automated Algorithm for Detecting Inaccurate and Imprecise Transitions in Multiple-Reaction Monitoring Mass Spectrometry (Mrm-Ms) |
D. R. Mani, Susan E. Abbatiello, Hasmik Keshishian, Steven A. Carr |
A |
19 |
| Development of Isoart As an Analysis Tool for Subtle Modification of Isotope Ratio Proteomics (Smirp) and Manipulation of 13C/12C Ratio in E. Coli. |
Puneet Souda, Arthur Laganowsky, Sara Bassilian, Jonathan Katz, Julian Whitelegge. |
A |
20 |
| Phosphoproteomic Analyses of Phosphorylation Sites in Membrane Fractions of 400 Mm High-Salt-Stressed Arabidopsis Thaliana |
Ing-Feng Chang, Shu-Ying Wang, Lan-Yu Wang, Jue-Liang Hsu |
A |
21 |
| Adapting Existing Proteomics Tools for Massively Parallel Peptide Discovery (Mppd) |
William Nelson, Kert Viele, Bert Lynn |
A |
22 |
| Modeling Contaminants in Tandem Affinity Purification Experiments |
Mathieu Lavallée-Adam, Philippe Cloutier, Benoit Coulombe, Mathieu Blanchette |
A |
23 |
| Boosting Peptide Identication Performance By Combining Many Search Engines, Spectral Matching, and Proteotypic and Physicochemical Peptide Properties. |
Prabhakar Gubbala, Nathan Edwards |
A |
24 |
| Proteogenomics of Zea mays: refining the genome annotation |
Natalie E Castellana, Zhouxin Shen, Laurie G. Smith, Steven P. Briggs, Vineet Bafna |
A |
25 |
| Computing Cross-Correlation of Sequest in Linear Time |
Hosung Jo, Taekyu Lee, Heejin Park, Eunok Paek |
A |
26 |
| Generic Comparison of Protein Inference Engine Families |
Manfred Claassen, Lukas Reiter, Michael O. Hengartner, Joachim M. Buhmann, Ruedi Aebersold |
A |
27 |
| Western Blot-Like Presentation of Gel-Enhanced Lc/Ms Data and Software-Based Detection of Protein Modifications |
Akiyasu C. Yoshizawa, Lixy Yamada, Hisaaki Taniguchi |
A |
28 |
| Reducing The Redundency and Enhancing The Quality of Ms2 Data |
Markus Müller, Erik Ahrne, Yuki Ohta, Frederic Nikitin, Frederique Lisacek |
A |
29 |
| Protein Surface Comparison Algorithm for Predicting Dna Binding Proteins - Using Estrogen Response Element (Ere) As a Model |
Po-Cheng Chuang, Po-Han Cheng, Hung-Yu Kao, Shu-Hui Chen, Mei-Ling Tsai |
A |
30 |
| Deconvolution of Complex Tandem Mass Spectra of Intact Proteins: a Combinatorial Approach |
Xiaowen Liu, Yuval Inbar, Pieter C. Dorrestein, Puneet Souda, Julian P. Whitelegge, Vineet Bafna And Pavel A. Pevzner |
A |
31 |
| MSPEP: A spectral alignment algorithm for the detection of post translational modifications |
Lijuan Mo, Yunhu Wan, Austin Yang, Ting Chen |
A |
32 |
| Automatic querying and identification of molecules by spatial localization in MALDI Mass Spectrometry Imaging. |
Jocelyne Bruand, Srinivas Sistla, Pieter Dorrestein, Majid Ghassemian, Céline Mériaux, Maxence Wisztorski, Isabelle Fournier, Michel Salzet, Terry Gaasterland,Eduardo Macagno, Vineet Bafna |
A |
33 |
| Improved de novo MS/MS peptide sequencing by subsequent pseudo database search and consensus spectrum variants |
Jian Liu, Johannes Hewel, Vicent Fong, Andrew Emili |
A |
34 |
| Statistical analysis of label-free comparative proteomics data using a logistic regression with an "elastic net" penalty. |
Mourad Mellal, Sabine Brugière, Sophie Lambert-Lacroix, Myriam Ferro, Daniel Salvi2, Norbert
Rolland, Jérome Garin, Christophe Masselon, and Anestis Antoniadis |
A |
35 |
| A Fast Method to Determine The Parameters for Fuzzy C--Means Cluster Validation |
Veit Schwämmle, Ole Nørregaard Jensen |
B |
1 |
| Quantitative Proteomics Analysis of Camp/Protein Kinase a (Pka)-Mediated Protein Changes in S49 Lymphoma Cells |
Yurong Guo, Lingzhi Zhang, Paul Insel, Susan Taylor |
B |
2 |
| Assessment of Ms Informatic Tools for Peptidomics: Peptide Identification and Relative Quantification. |
Steven Taylor |
B |
3 |
| Simultaneous Quantification of Histone Multisite Modifications By Lc/Ms/Ms-Mrm |
Kangling Zhang, Agus Darmanto, Guoliang Xu. |
B |
4 |
| Performance and Uncertainty in The Measurements of Quantitative Proteomics Using Stable Isotope Labeling With Amino Acids in Cell Culture |
Xin Huang, Aleksey V. Tolmachev, Miao Liu, Yulei Shen, Gordon A. Anderson, Kai Fu, Shi-Jian Ding |
B |
5 |
| Improved quantitative analysis of mass spectrometry using quadratic equations |
Joo Young Yoon, Kyung Young Lim, Sunho Lee, Kunsoo Park, Eunok Paek, Un-Beom Kang, Jeonghun Yeom, Cheolju Lee |
B |
6 |
| Iomiqs Integration of Mass Spectra Identification and Quantification Software |
Julia Weiß, Timo Mühlhaus, Dorothea Hemme, Frederik Sommer, Michael Schroda |
B |
7 |
| Precursor Ion Mass Spectra Comparison With Matlab Script Trego6.M |
Larry Gross, Audrey ONeill, Alexandra Newton, Xiaokun Shu, Roger Tsien |
B |
8 |
| Statistical Modeling of Spectral Count Data for Filtering High Confidence Interactions From Ap-Ms/Ms |
Hyungwon Choi, Anne-Claude Gingras, Zhaohui S. Qin, Alexey I. Nesvizhskii |
B |
9 |
| Bioinformatics for Label-Free Quantitative Proteomics: High-Throughput Automation Through Innovative Interconnection of Existing Open Source Software |
Andrej Vasilj, Marc Gentzel, Andrej Shevchenko |
B |
10 |
| Characterization of Cochlea Proteome to Study Hearing Loss Phenomenon in Usher Syndrome 1 |
Parminder Kaur, Giridharan Gokulrangan, Rebecca Levinson, Kumar Alagramam, Mark R Chance |
B |
11 |
| Comparison of Open Source Quantification Tools for Analysis of Large Sets of Lc/Ms/Ms Data |
L. Renee Olano, Dhaval Nanavati, Anthony J. Makusky, Jeffrey A. Kowalak, Sanford P. Markey |
B |
12 |
| Multiple Hierarchical Linear Models and Label-Free Quantitative Proteomics to Identify Differentially Expressed Proteins in Breast Cancer |
Richard Leduc, Michael Boyne, R. Reid Townsend, Ron Bose |
B |
13 |
| Automated Grouping and Quantification of Anonymous Mass-Tagged Peptide Ions Using Picquant |
Ken G. Victor, Charles E. Lyons, Sergey Moshnikov, Dennis J. Templeton |
B |
14 |
| Speeding Up Peptide and Protein Identification Via Tandem Mass Spectrometry By Suffix Arrays |
Chen Zhou, Hao Chi, Le-Heng Wang, You Li, Yan-Jie Wu, Yan Fu, Rui-Xiang Sun, Si-Min He |
B |
15 |
| Global Proteomics Approaches to Identify Urinary Proteins That Distinguish Pancreatic Cancer From Chronic Pancreatitis |
Senait Asmellash, Kyoko Kojima, Chinatsu Kojima, Christopher Shubert, Liuyan Yang, Christopher Klug, James Mobley, John Christein |
B |
16 |
| Improved Identification of Phosphopeptides From Etd/Ecd Ms Data Using Robust Twin Boosting |
Shan He, John K. Heath And Helen J. Cooper |
B |
17 |
| Cross Platform Comparison of a Static and Dynamic Range Proteomic Mixture Refined With Multiple Search Engines, Parameters and Software Platforms. |
Archer D Smith Iv, Gregory J. Bowersock, Kristie Rose, Jennifer Busby, Stephen Barnes, Matthew B. Renfrow, James A. Mobley |
B |
18 |
| Capturing Transient Biosynthetic Intermediates on The Post-Translationally Modified Polyketide Synthase Responsible for The Biosynthesis of Lovastatin By Ft-Icr-Ms. |
Michael J. Meehan, Pieter C. Dorrestein |
B |
19 |
| Proteofit: a Bundle of Vba Macros for Parsing, Filtering and Analyzing Mascot Database Search Results for Large-Scale Proteomics. |
Takako Taniguchi, Hisaaki Taniguchi |
B |
20 |
| A Bayesian Approach to The Quantification of Overlapping Peptides in a Mass Spectrum |
Qi Zhu, Adetayo Kasim, Dirk Valkenborg, Tomasz Burzykowski |
B |
21 |
| An R Package for Protein Quantification in Label-Free Lc-Ms Experiments |
Timothy Clough, Ching-Yun Chang, Susanne Ragg, Olga Vitek |
B |
22 |
| Comparison of Statistical Methods for Protein Quantification in Lc-Ms and Srm Experiments |
Ching-Yun Chang, Timothy Clough, Paola Picotti, Ruedi Aebersold, Olga Vitek |
B |
23 |
| Statistical Methods for Protein Quantification in Srm Experiments |
Ching-Yun Chang, Timothy Clough, Paola Picotti, Ruedi Aebersold ,Olga Vitek |
B |
24 |
| C-Terminal Sequence Analysis in The Proteomic Era |
Pablo Moerman, Bart Devreese , Bart Samyn. |
B |
25 |
| Quantitative Local False Discovery Rates, Deep Sampling, Protein Abundance Change and a Signed Log-Likelihood Test Applied to Microbial Proteomes |
David A. C. Beck, Qiangwei Xia, Erik L. Hendrickson, Tiansong Wang, Marina Meila, Murray Hackett |
B |
26 |
| Evaluation of Relative and Absolute Quantification in Shotgun Proteomics With Label-Free Methods |
Doro Rutishauser, Jonas Grossmann, Bernd Roschitzki, Christian Panse, Simon Barkow-Oesterreicher, Claudia Fortes, Ralph Schlapbach |
B |
27 |
| Pkdaclass: Open Source Software for Analyzing Maldi-Tof Data |
Juliet N. Ndukum, Mourad Atlas, And Susmita Datta |
B |
28 |
| Systematic Discovery of Nitrated Motifs in Nitroproteomics Data By Computational Methods |
Jeong Won Kang, Hyo A Kang, Jae Kyung Kim, Dongsup Kim, Kwang Pyo Kim |
B |
29 |
| Normalized Protein Quantification Web Service (Norpq) for Ms-Based Stable Isotope Labeling- a Validated Website for Dimethyl Labeling |
Chang-Wu Chen, Po-Tsun Shen, Yen-Wen Chen, Shu-Hui Chen |
B |
30 |
| Moda - Spectral Alignment for The Fast Unrestrictive Identification of Multiply-Modified Peptides Using Ms/Ms Data |
Seungjin Na, Nuno Bandeira, Eunok Paek |
B |
32 |
| The Construction and Application of Normalized Svr Retention Time Predictor for Validation of Neuropeptide Identification By De Novo Sequencing |
Weifeng Cao, Lingjun Li |
B |
33 |
