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ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis

Nikolas Kessler, Frederik Walter, Marcus Persicke, Stefan P. Albaum, Jörn Kalinowski, Alexander Goesmann, Karsten Niehaus, Tim W. Nattkemper, Frederique Lisacek
2014 PLoS ONE  
Quantitation of metabolites is hampered by matrix effects and nonlinear responses in LC-ESI-MS measurements.  ...  Adduct formation, fragmentation events and matrix effects impose special challenges to the identification and quantitation of metabolites in LC-ESI-MS datasets.  ...  complex LC-ESI-MS spectra.  ... 
doi:10.1371/journal.pone.0113909 pmid:25426929 pmcid:PMC4245236 fatcat:u7fuqaqlovgnjb3uyj7lcfjicu

Evaluation of female Aedes aegypti proteome via LC-ESI-MS/MS using two protein extraction methods

Abubakar Shettima, Intan H Ishak, Syahirah Hanisah Abdul Rais, Hadura Abu Hasan, Nurulhasanah Othman
2021 PeerJ  
Then, protein identification was performed by LC-ESI-MS/MS and followed by functional protein annotation analysis.  ...  LC-ESI-MS/MS identified 1,290 and 890 proteins from the CytoBusterTM reagent and TCA acetone precipitation, respectively.  ...  LC-ESI-MS/MS data of this study is available at proteomeXchange with identifier number PXD019698.  ... 
doi:10.7717/peerj.10863 pmid:33717682 pmcid:PMC7936558 fatcat:qxsol3dt3zb75marfkdvfkfemy

Phytochemical Diversity in Rhizomes of Three Reynoutria Species and their Antioxidant Activity Correlations Elucidated by LC-ESI-MS/MS Analysis

Izabela Nawrot-Hadzik, Sylwester Ślusarczyk, Sebastian Granica, Jakub Hadzik, Adam Matkowski
2019 Molecules  
Furthermore, compounds tentatively annotated as lignin oligomers were observed for the first time in the studied species. The rhizomes of all Reynoutria species exhibited strong antioxidant activity.  ...  Our studies confirmed the presence of procyanidins with high degree of polymerization, up to decamers, in the rhizomes of R. japonica and provides new data on the presence of these compounds in other Reynoutria  ...  Compounds 14 and 26 possessed doublecharged ion with signals at m/z 720 [M − 2H] 2− and compound 31, double-charged ion with signals at m/z 1008 [M − 2H] 2− .  ... 
doi:10.3390/molecules24061136 fatcat:a2xi62mq5nhn7n4ezg4ib2dx64

Proteome analysis of excretory-secretory proteins of Entamoeba histolytica HM1:IMSS via LC–ESI–MS/MS and LC–MALDI–TOF/TOF

Jorim Anak Ujang, Soon Hong Kwan, Mohd Nazri Ismail, Boon Huat Lim, Rahmah Noordin, Nurulhasanah Othman
2016 Clinical Proteomics  
The ES proteins were identified using two mass spectrometry tools, namely, LC-ESI-MS/MS and LC-MALDI-TOF/TOF.  ...  Of the 219 proteins, 89 were identified by both mass-spectrometry systems, while 112 and 18 proteins were detected exclusively by LC-ESI-MS/MS and LC-MALDI-TOF/TOF respectively.  ...  In addition, this study is partly supported by HiCOE program, Malaysian Ministry of Higher Education.  ... 
doi:10.1186/s12014-016-9135-8 pmid:27895543 pmcid:PMC5120466 fatcat:bjsirkkjtvfjxhuaqnmqd2zoa4

Pericardial fluid proteomic label-free quantification of differentially expressed proteins in ischemic heart disease patients with systolic dysfunction by nano-LC-ESI-MS/MS analysis

Junaid Ullah, Satwat Hashmi, Arslan Ali, Faisal Khan, Shahid Ahmed Sami, Nageeb Basir, Syeda Saira Bokhari, Hasanat Sharif, Hesham R. El-Seedi, Syed Ghulam Musharraf
2021 RSC Advances  
Proteomics of pericardial fluid from patients with ischemic heart disease having impaired systolic function.  ...  Acknowledgements This work was supported by the Pakistan Academy of Sciences (Grant # 5-9/PAS/745).  ...  Arsalan Tahir, Mass spectrometry section, ICCBS, for their assistance in nano-LC-MS/MS analysis.  ... 
doi:10.1039/d0ra08389e pmid:35423047 pmcid:PMC8691035 fatcat:b5xuqjgs7vamzmjvnkgmfzhkam

Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host

Ana G. Abril, Mónica Carrera, Karola Böhme, Jorge Barros-Velázquez, Benito Cañas, Jose L. R. Rama, Tomás G. Villa, Pilar Calo-Mata
2020 Frontiers in Microbiology  
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus  ...  functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.  ...  MC is supported by the Ramón y Cajal contract (Ministry of Science and Innovation of Spain).  ... 
doi:10.3389/fmicb.2020.01241 pmid:32582130 pmcid:PMC7296060 fatcat:gstean4625dz3fkfn6citlzhza

Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

Christopher Ashwood, Chi-Hung Lin, Morten Thaysen-Andersen, Nicolle H. Packer
2018 Journal of the American Society for Mass Spectrometry  
We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released Nand O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/ MS.  ...  These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates.  ...  PGC-LC-ESI-MS/MS Glycan Analysis MS Parameters For the Agilent 3D ion trap, glycans were analyzed according to these MS conditions: m/z 350-2200, 5 microscans, m/z Data Availability In order to adhere  ... 
doi:10.1007/s13361-018-1932-z pmid:29603058 fatcat:bvw4zo5k7rc5nftz4hlkqog36e

Phytochemical Screening by LC-ESI-MS/MS and Effect of the Ethyl Acetate Fraction from Leaves and Stems of Jatropha macrantha Müll Arg. on Ketamine-Induced Erectile Dysfunction in Rats

Johnny Aldo Tinco-Jayo, Enrique Javier Aguilar-Felices, Edwin Carlos Enciso-Roca, Jorge Luis Arroyo-Acevedo, Oscar Herrera-Calderon
2021 Molecules  
The phytochemical constituents were determined by LC-ESI-MS/MS, the total phenolic compounds and total flavonoids (TPC and TF) by Folin-Ciocalteu and aluminum chloride, respectively.  ...  The aim of this study was to determine the phytochemical constituents in leaves and stems ethyl acetate fraction (LEAF and SEAF) of J. macrantha and to compare the antioxidant activity and the ameliorative  ...  Conflicts of Interest: The authors declare no conflict of interest. Sample Availability: Samples of the compounds are available from the authors.  ... 
doi:10.3390/molecules27010115 pmid:35011347 pmcid:PMC8746923 fatcat:wskivdnkyjdnfap3kyqa4cccau

Identification of Conus amadis disulfide isomerase: minimum sequence length of peptide fragments necessary for protein annotation

Konkallu Hanumae Gowd, K. S. Krishnan, Padmanabhan Balaram
2007 Molecular Biosystems  
Analysis of tryptic fragments by MALDI-MS/MS and LC-ESI-MS/MS methods permits sequence assignment.  ...  Sequences of length ¢7 residues provide unambiguous identification in conjunction with protein molecular mass as a filter.  ...  The mass spectrometric facilities at IISc, Bangalore are supported under the Proteomics program funded by the Department of Biotechnology, Government of India. We acknowledge Y. K.  ... 
doi:10.1039/b705382g pmid:17639131 fatcat:vjfveaj3hjas3pizowywlbju6y

Identification of the protein sequence of the type III effector XopD from the B100 strain ofXanthomonas campestrispvcampestris

Joanne Canonne, Carole Pichereaux, Daniel Marino, Dominique Roby, Michel Rossignol, Susana Rivas
2012 Plant Signalling & Behavior  
Here, we describe the identification of the complete protein sequence of XopD XccB100 , which presents an N-terminal extension of 40 amino acids with respect to the protein annotated in public databases  ...  This protein interaction leads to inhibition of AtMYB30 transcriptional activity and promotion of bacterial virulence.  ...  Following electrophoresis and Coomassie staining of the gel, a~90 kDa band corresponding to XopD XccB100 was excised, digested with trypsin and analyzed by mass spectrometry (Nano LC/ESI MS/MS).  ... 
doi:10.4161/psb.18828 pmid:22353870 pmcid:PMC3405711 fatcat:qipt2w2hlbal7nvqivi4wipqwy

MALDI mass spectrometry imaging of N -glycans on tibial cartilage and subchondral bone proteins in knee osteoarthritis

Matthew T. Briggs, Julia S. Kuliwaba, Dzenita Muratovic, Arun V. Everest-Dass, Nicolle H. Packer, David M. Findlay, Peter Hoffmann
2016 Proteomics  
MALDI mass spectrometry imaging of N-glycans on tibial cartilage and subchondral bone proteins in knee osteoarthritis Publishing in a subscription based journal Accepted (peer-reviewed) Version The accepted  ...  version of an article is the version that incorporates all amendments made during the peer review process, but prior to the final published version (the Version of Record, which includes; copy and stylistic  ...  Figure 2 : 2 (a) LC-ESI-MS profiles of bone marrow and cartilage regions, and (b) MALDI-MS profiles of bone marrow 189 and cartilage regions, annotated with confirmed N-glycan structures from LC-ESI-MS  ... 
doi:10.1002/pmic.201500461 pmid:26992165 fatcat:ebzyqj3l6fgmplr57dwcox5jua

Identification of annotated metabolites in the extract of Centella asiatica

Rani Komal, Tyagi Mitali, Singh Akanksha, Shanmugam Vairamani, Shanmugam Annaian, Pillai Manoj, Srinivasan Alagiri
2019 Journal of Medicinal Plants Research  
The compounds were identified using liquid chromatography-mass spectrometry with database confirmation. 3,201 compounds were identified using the METLIN database.  ...  Plants contribute to 75% of molecular medicines (MM) either directly or indirectly. Centella asiatica (CA) is being extensively used in experimental and clinical studies.  ...  Figure 3 . 3 Quantification of cytarabine and methotrexate using LC-ESI-MS/MS.  ... 
doi:10.5897/jmpr2018.6711 fatcat:gmyc2m3c6bctdmgnakflasjhoy

MALDI Mass Spectrometry Imaging of Early‐ and Late‐Stage Serous Ovarian Cancer Tissue Reveals Stage‐Specific N‐ Glycans

Matthew T. Briggs, Mark R. Condina, Yin Ying Ho, Arun V. Everest‐Dass, Parul Mittal, Gurjeet Kaur, Martin K. Oehler, Nicolle H. Packer, Peter Hoffmann
2019 Proteomics  
Tumor-specific N-glycans are identified and structurally characterized by porous graphitized carbon-liquid chromatography-electrospray ionization-tandem mass spectrometry (PGC-LC-ESI-MS/MS), and then assigned  ...  The distribution of these markers is evaluated using a tissue microarray of early- and late-stage patients.  ...  using PGC-LC-ESI-MS/MS.  ... 
doi:10.1002/pmic.201800482 pmid:31364262 fatcat:d4eql57yxrbjtf4whmqpkf6k5i

Pattern Recognition and Pathway Analysis with Genetic Algorithms in Mass Spectrometry Based Metabolomics

Wei Zou, Vladimir Tolstikov
2009 Algorithms  
Three independent and complementary analytical techniques for metabolic profiling were applied: hydrophilic interaction chromatography (HILIC-LC-ESI-MS), reversed-phase liquid chromatography (RP-LC-ESI-MS  ...  Metabolites putatively detected with LC-ESI-MS profiling require further elemental composition assignment with accurate mass measurement by Fourier-transform ion cyclotron resonance mass spectrometry (  ...  We are grateful to Professor David Neale from Department of Plant Sciences and Professor Robert Weiss from Department of Internal Medicine of UC Davis for providing samples and corresponding descriptive  ... 
doi:10.3390/a2020638 fatcat:s3dqmtdtovdalmo6n2qqmzacr4

Comparative testis proteome dataset between cattleyak and yak

Fang Yang, TserangDonko Mipam, Lei Sun, Shumin Yu, Xin Cai
2016 Data in Brief  
(LC-ESI-MS/MS).  ...  All the DEPs were subjected to functional classification by Gene Ontology (GO) analysis and gene-pathway annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG).  ...  We also gratefully acknowledge the financial support of the Grants from the National Natural Science Foundation of China (31172379 and 31572396).  ... 
doi:10.1016/j.dib.2016.05.071 pmid:27366779 pmcid:PMC4910294 fatcat:ogj2ea5s7jej3ifayxholzjrte
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