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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.  ...  Glycoproteomics involves the study of the glycosylation events on protein sequences ranging from purified proteins to whole proteome scales.  ...  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

Intelligence Algorithms for Protein Classification by Mass Spectrometry

Zichuan Fan, Fanchen Kong, Yang Zhou, Yiqing Chen, Yalan Dai
2018 BioMed Research International  
Preprocessing algorithms have been also studied, as these methods are useful for feature selection or feature extraction to improve classification performance.  ...  Protein MS data growing with data volume becomes complicated and large; improvements in classification methods in terms of classifier selection and combinations of different algorithms and preprocessing  ...  Acknowledgments The authors wish to express their gratitude for Fundamental Research Funds for the Central Universities, China (No. XDJK2016C150), and Southwest University (No.  ... 
doi:10.1155/2018/2862458 fatcat:cbbxhjurunftbmnlxmpfkjhfrm

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.  ...  De novo peptide sequencing algorithms have been widely used in proteomics to analyse tandem mass spectra (MS/MS) and assign them to peptides, but quality-control methods to evaluate the confidence of de  ...  The effective fitness function let GP to generate a strong discriminative scoring function which was able to improve the peptide identification. The GP method learns from thousands of MS/MS spectra.  ... 
arXiv:1908.08010v1 fatcat:rih5eyajlrgh5fnkzg76rioidm

Methodologies and experimental platforms for generating and analysing microarray and mass spectrometry-based omics data to support P4 medicine

Pietro H. Guzzi, Giuseppe Agapito, Marianna Milano, Mario Cannataro
2015 Briefings in Bioinformatics  
P4 medicine presupposes the elucidation of the so-called omic world, under the assumption that this knowledge may explain differences of patients with respect to disease prevention, diagnosis and therapies  ...  After introducing basic concepts of P4 medicine and omics sciences, we review some computational tools and approaches for analysing selected omics data, with a special focus on microarray and mass spectrometry  ...  The pipeline contains programs for: (i) spectra handling, i.e. interfacing with the different binary formats and translating them into a standard format; (ii) probabilistic peptide identification; (iii  ... 
doi:10.1093/bib/bbv076 pmid:26351205 fatcat:lehrewonvfepnd33cbefzl5mci

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

Jia Zhang, Ming-kun Yang, Honghui Zeng, Feng Ge
2016 Molecular & Cellular Proteomics  
We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases.  ...  With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events.  ...  Tandem (67), MSAmanda (68) , and MSGF (69) , have been deployed within this step to improve the sensitivity for peptide identifications.  ... 
doi:10.1074/mcp.m116.060046 pmid:27630248 pmcid:PMC5098048 fatcat:rjvarp6vyrbtdiyilihoyb5oza

Recent Trends in Data Mining in Proteomics and Various Applications of Mass Spectrometry in Proteomic Studies

Siva Kishore Nandikolla, Satya Varali M
2011 Journal of Bacteriology & Parasitology  
Several projects were initiated by the Human Proteome Organization (HUPO) aiming for the proteome analysis of distinct human organs.  ...  The relevant bioinformatics data is drawn from the inter-laboratory comparisons as well as from the rechecking of all data sets submitted  ...  This technology can generate huge amount of raw mass spectra and/or tandem mass spectra.  ... 
doi:10.4172/jpb.s11-001 fatcat:f2hk7neg5ngpthfgv5w75iptzy

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data [article]

Peter Lasch, Andy Schneider, Christian Blumenscheit, Joerg Doellinger
2019 bioRxiv   pre-print
For example, LC-tandem mass spectrometry (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at  ...  Over the past decade, modern methods of mass spectrometry (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms.  ...  Genetic algorithms, for example, could be advantageously applied to identify combinations of taxonspecific peptide markers and could thus contribute to improve the accuracy of identification. Fig.  ... 
doi:10.1101/870089 fatcat:irngefddqnharedgutjicilhnm

Application of Computational Proteomics and Lipidomics in Drug Discovery

Nitish Kumar Mishra, Mamta Shukla
2016 Journal of Theoretical and Computational Science  
Information about spectrum of target Abstract The process of drug discovery requires integration of biochemical and genetic tests to analyze the effects of drug molecules on biological systems.  ...  Lipidomics or proteomics are not only used for target identification and deconvolution but also for analysis of off-targets and for studying the mode of action of drug molecules.  ...  InsPecT InsPecT is a tool to identify posttranslationally modified peptides from tandem mass spectra [84] .  ... 
doi:10.4172/2376-130x.1000105 fatcat:kv3tv524yza6nishayuwdtdxrm

A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics

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
2013 Molecular Brain  
Results: Over fifty isotopically resolved ion signals in the peptide mass range are reproducibly observed across experiments.  ...  Both the identification and functional characterization of specific neuropeptides are ongoing fields of research.  ...  JNA, KJB, and JPS analyzed the data, prepared the figures, and wrote the manuscript. All authors have read and given approval to the final version of the manuscript.  ... 
doi:10.1186/1756-6606-6-60 pmid:24373546 pmcid:PMC4022047 fatcat:vu7wbdinfbddvahs7bpkwc6kxq

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Libraries

Peter Lasch, Andy Schneider, Christian Blumenscheit, Joerg Doellinger
2020 Molecular & Cellular Proteomics  
For example, LC-tandem mass spectrometry (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at  ...  Over the past decade, modern methods of mass spectrometry (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms.  ...  Genetic algorithms, for example, could be advantageously applied to identify combinations of taxon-specific peptide markers and could thus contribute to improve the accuracy of microorganism identification  ... 
doi:10.1074/mcp.tir120.002061 pmid:32998977 pmcid:PMC7710138 fatcat:sjaadp5kgzaytcwr4bkucu2ym4

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, Andrés Ritter, Régis Lavigne, Dominique Marie, Pierre Peterlongo, Philippe Potin, Charles Pineau
2019 BMC Genomics  
Results: Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles.  ...  ., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism.  ...  Acknowledgements We are grateful to Laurence Dartevelle and Susana Coelho for the production of unialgal Ec 32, Ec 410 and mutant oro of Ectocarpus.  ... 
doi:10.1186/s12864-019-5431-9 fatcat:hppqncrbmjfahp27ybnbfqdk7y

Liquid chromatography mass spectrometry-based proteomics: Biological and technological aspects

Yuliya V. Karpievitch, Ashoka D. Polpitiya, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney
2010 Annals of Applied Statistics  
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism.  ...  In the most widely used "bottom-up" approach to proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical  ...  Portions of this work were supported by the NIH R25-CA-90301 training grant in biostatistics and bioinformatics at TAMU, the National Institute of Allergy and Infectious Disease NIH/DHHS through interagency  ... 
doi:10.1214/10-aoas341 pmid:21593992 pmcid:PMC3095207 fatcat:bgwpk5tflzebdbws23oppbcxvy

Bioinformatics Applied to Proteomics [chapter]

Simone Cristoni, Silvia Mazzuc
2011 Systems and Computational Biology - Bioinformatics and Computational Modeling  
peaksonline DeNov Lutefis Open source,free http://www.hairyfatguy.com/Lutefisk/ DeNov SEQUES Commercial http://fields.scripps.edu/sequest databas searchin XTandem Open source,free http://www.thegpm.org/tandem  ...  It has been presented a novel scoring method for de novo interpretation of peptides from tandem mass spectrometry data.  ...  A selection of novel technologies come out that are now permitting researchers to identify the genetic background of crop improvement, explicitly the genes that contribute to the improved productivity  ... 
doi:10.5772/23680 fatcat:hwwvvyil5rhzlcmcqw6ot6ei74

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

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.  ...  Thus, a practical use of the open search strategy has been realized by Open-pFind for the truly global-scale proteomics experiments of today and in the future.  ...  Secondly, m tandem mass spectra are generated by copying the MS/MS information of the original spectra and assigning m different precursor ions (monoisotopic masses and charge states) to m tandem mass  ... 
doi:10.1101/285395 fatcat:fhbx7alh4fdw5ne3s5zcyvprru
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