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Improving the Results of De novo Peptide Identification via Tandem Mass Spectrometry Using a Genetic Programming-based Scoring Function for Re-ranking Peptide-Spectrum Matches [article]

Samaneh Azari, Bing Xue, Mengjie Zhang, Lifeng Peng
2019 arXiv   pre-print
Here, we propose a genetic programming (GP) based method, called GP-PSM, to learn a PSM scoring function for improving the rate of confident peptide identification from MS/MS data.  ...  A fundamental part of a quality-control method is the scoring function used to evaluate the quality of peptide-spectrum matches (PSMs).  ...  Conclusions and Future Work This work developed a genetic programming (GP) based method to automatically generate a PSM scoring function aiming at reducing the rate of false discovery peptide identification  ... 
arXiv:1908.08010v1 fatcat:rih5eyajlrgh5fnkzg76rioidm

Recent developments in quantitative proteomics

Christopher H. Becker, Marshall Bern
2011 Mutation Research. Genetic Toxicology and Environmental Mutagenesis  
The primary emphasis is on the combination of liquid chromatography-mass spectrometry (LC-MS) methods and associated tandem mass spectrometry (LC-MS/MS).  ...  Then a discussion follows on the various computational techniques used to identify peptides and proteins from LC-MS/MS data.  ...  Acknowledgments The authors are pleased to acknowledge the many contributions of Drs.  ... 
doi:10.1016/j.mrgentox.2010.06.016 pmid:20620221 pmcid:PMC2980806 fatcat:42hsowazinhb5ib3uo6h25qfqu

Algorithms and design strategies towards automated glycoproteomics analysis

Han Hu, Kshitij Khatri, Joseph Zaia
2016 Mass spectrometry reviews (Print)  
and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods.  ...  , as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts.  ...  ACKNOWLEDGEMENTS The authors were supported by NIH grant P41RR10888, R01HL098950, and R21CA177479. Abbreviations API  ... 
doi:10.1002/mas.21487 pmid:26728195 pmcid:PMC4931994 fatcat:oxin253k2nhhtbvohx6ksyxkgi

NBPMF: Novel network-based inference methods for peptide mass fingerprinting

Zhewei Liang, Gilles Lajoie, Kaizhong Zhang
2017 2017 IEEE 16th International Conference on Cognitive Informatics & Cognitive Computing (ICCI*CC)  
Moreover, we use linear regression to adjust the matching score according to the masses of proteins. In addition, we consider the order of retention time to further correct the score function.  ...  In this thesis, we developed a novel network-based inference software termed NBPMF. By analyzing peptide-protein bipartite network, we designed new peptide protein matching score functions.  ...  The next processing is peptide de novo sequencing, which derives the peptide sequence from the tandem mass spectrum without the need of a sequence database.  ... 
doi:10.1109/icci-cc.2017.8109752 dblp:conf/IEEEicci/LiangLZ17 fatcat:4bssuvd53jc2bgd4ckgufg4dn4

De Novo MS/MS Sequencing of Native Human Antibodies

Adrian Guthals, Yutian Gan, Laura Murray, Yongmei Chen, Jeremy Stinson, Gerald Nakamura, Jennie R Lill, Wendy Sandoval, Nuno Bandeira
2016 Journal of Proteome Research  
In this proof-of-concept study, we demonstrate the feasibility of a novel MS/MS antibody discovery approach in which only serum antibodies are required, without the need for sequencing of genetic material  ...  Although it has been demonstrated that tandem mass spectrometry (MS/MS) techniques can interrogate the full polyclonal antibody (pAb) response to an antigen in vivo, all current approaches identify MS/  ...  Although FDR cannot be accurately estimated when searching against de novo sequences, resulting peptide-spectrum matches (PSMs) were useful for estimating what percentage of residues in each full-length  ... 
doi:10.1021/acs.jproteome.6b00608 pmid:27779884 pmcid:PMC5574256 fatcat:mgpjishm2zecxd673wnxbcfthu

JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells

Yuxin Li, Xusheng Wang, Ji-Hoon Cho, Timothy I. Shaw, Zhiping Wu, Bing Bai, Hong Wang, Suiping Zhou, Thomas G. Beach, Gang Wu, Jinghui Zhang, Junmin Peng
2016 Journal of Proteome Research  
Then the JUMPg program is applied to process a label-free mass spectrometry dataset of Alzheimer's disease postmortem brain, uncovering 496 new peptides of amino acid substitutions, alternative splicing  ...  de novo assembly.  ...  Acknowledgments The authors thank for all other members in the Peng  ... 
doi:10.1021/acs.jproteome.6b00344 pmid:27225868 pmcid:PMC5033046 fatcat:emn4dthfabgufjg4zd5p3sbwrm

Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics [article]

Hao Chi, Chao Liu, Hao Yang, Wen-Feng Zeng, Long Wu, Wen-Jing Zhou, Xiu-Nan Niu, Yue-He Ding, Yao Zhang, Rui-Min Wang, Zhao-Wei Wang, Zhen-Lin Chen (+7 others)
2018 bioRxiv   pre-print
Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified.  ...  In this search results, Open-pFind also excelled in an independent test for false positives based on the presence or absence of olfactory receptors.  ...  Wang, L.H. et al. pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun Mass Spectrom 21, 2985-2991 (2007). 36.  ... 
doi:10.1101/285395 fatcat:fhbx7alh4fdw5ne3s5zcyvprru

Identification of post-translational modifications via blind search of mass-spectra

D. Tsur, S. Tanner, E. Zandi, V. Bafna, P.A. Pevzner
2005 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)  
We use MS-Alignment to construct a two-dimensional PTM frequency matrix that reflects the number of MS/MS spectra in a sample for each putative PTM type and each amino acid.  ...  The blind PTM identification opens a possibility to study the extent and frequency of different types of PTMs, still an open problem in proteomics.  ...  Introduction Fueled by recent improvements in instrumentation and software, tandem mass spectrometry has become the tool of choice for protein identification.  ... 
doi:10.1109/csb.2005.34 dblp:conf/csb/TsurTZBP05 fatcat:3m6nz3wmqzaedd2y7deftnhcju

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

Charles Ansong, Nikola Tolić, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith (+4 others)
2011 BMC Genomics  
Conclusion: This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive  ...  Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.  ...  This work was supported in part by the National Institute of Allergy and Infectious Diseases NIH/DHHS through interagency agreement Y1-AI-8401-01 (project website http://www.SysBEP.org with links to raw  ... 
doi:10.1186/1471-2164-12-433 pmid:21867535 pmcid:PMC3174948 fatcat:jldhlcg5cjathcm2dnonp3s4yu

Proteomic Cancer Classification with Mass Spectrometry Data

Jagath C Rajapakse, Kai-Bo Duan, Wee Kiang Yeo
2005 American Journal of Pharmacogenomics  
A number of de novo sequencing and Classification software programs are based on a graph theory approach [60] [61] [62] [63] in which a NC-spectrum graph is created ('NC' is an abbreviation for Support  ...  first, one can try to interpret the spectra directly to ProFound [71] is an expert system for protein identification using infer a peptide amino acid sequence using the so-called 'de novo Bayesian theory  ... 
doi:10.2165/00129785-200505050-00001 pmid:16196498 fatcat:srtqlyws5rcybi5hkjkyarojc4

Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences

Gloria M. Sheynkman, Michael R. Shortreed, Brian L. Frey, Mark Scalf, Lloyd M. Smith
2013 Journal of Proteome Research  
However, such variant peptides are not generally detected in standard proteomic analyses, due to their absence from the generic databases that are employed for mass spectrometry searching.  ...  Here, we extend previous work that demonstrated the use of customized SAP databases constructed from sample-matched RNA-Seq data.  ...  This research was also supported in part by National Science Foundation Grant CHE-0840494 through use of the University of Wisconsin-Madison chemistry computing resources.  ... 
doi:10.1021/pr4009207 pmid:24175627 pmcid:PMC3947302 fatcat:cbjv3pxwwbchzc4oxmllezkeam

LC–MS Based Detection of Differential Protein Expression

Leepika Tuli, Habtom W. Ressom
2009 Journal of Proteomics & Bioinformatics  
While several techniques are available in proteomics, LC-MS based analysis of complex protein/peptide mixtures has turned out to be a mainstream analytical technique for quantitative proteomics.  ...  Significant technical advances at both sample preparation/separation and mass spectrometry levels have revolutionized comprehensive proteome analysis.  ...  Membership Grant, and the Prevent Cancer Foundation Grant awarded to HWR.  ... 
doi:10.4172/jpb.1000102 pmid:20473349 pmcid:PMC2867618 fatcat:weyv7yegwjhlnotanbmsm7fjca

Deep learning in proteomics

Bo Wen, Wenfeng Zeng, Yuxing Liao, Zhiao Shi, Sara R Savage, Wen Jiang, Bing Zhang
2020 Proteomics  
With the recent advancements of the tandem mass spectrometry (MS) technology, protein expression and post-translational modifications (PTMs) can be studied in a variety of biological systems at the global  ...  Here, we provide a comprehensive overview of deep learning applications in proteomics including retention time prediction, MS/MS spectrum prediction, de novo peptide sequencing, PTM prediction, major histocompatibility  ...  By considering the predicted spectra based on deep learning, pNovo3 re-ranks the peptide candidates generated by pNovo+ (a spectrum-graph and dynamic programming based algorithm [89] ) using a learning-to-rank  ... 
doi:10.1002/pmic.201900335 pmid:32939979 fatcat:gq6yffww6reu7eqrky7u6l2454

Purification and characterization of transcription factors

L.I. Nagore, R.J. Nadeau, Q. Guo, Y.L.A. Jadhav, H.W. Jarrett, W.E. Haskins
2013 Mass spectrometry reviews (Print)  
However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry  ...  Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and  ...  Acknowledgments We thank the RCMI program at UTSA (NIH 5G12RR013646-12) and NIH grant 1R01GM043609 (to H. W. Jarrett) for support.  ... 
doi:10.1002/mas.21369 pmid:23832591 pmcid:PMC3758410 fatcat:t3wsugpbgfco7jl5gseaqg2isi

Protein Analysis by Shotgun/Bottom-up Proteomics

Yaoyang Zhang, Bryan R. Fonslow, Bing Shan, Moon-Chang Baek, John R. Yates
2013 Chemical Reviews  
Acknowledgments We gratefully thank Claire Delahunty and Xuemei Han for their critical review of this manuscript and constructive comments and suggestions.  ...  Funding was provided by the following NIH grants P41 GM103533/P41 RR011823, R01 DK074798, R01 HL079442, and R01 MH067880. Biographies Author Photos and Biographies.  ...  The peptide candidates are ranked and filtered to create peptide spectrum matches (PSMs) and peptide identifications.  ... 
doi:10.1021/cr3003533 pmid:23438204 pmcid:PMC3751594 fatcat:rmscemj4fvgjzbpg5u2b7qtsnu
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