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Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra

D. Mantini, F. Petrucci, P. Del Boccio, D. Pieragostino, M. Di Nicola, A. Lugaresi, G. Federici, P. Sacchetta, C. Di Ilio, A. Urbani
2007 Bioinformatics  
The method is validated on simulated and experimental data for demonstrating its capability of correctly extracting protein profiles from MALDI-TOF mass spectra.  ...  We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling.  ...  ACKNOWLEDGEMENTS We are particularly grateful to Enzo Ballone and Gian Luca Romani for continuous support and scientific discussion.  ... 
doi:10.1093/bioinformatics/btm533 pmid:18003646 fatcat:ewhuksgp35ejdcwdu3asv6d6fy

Proteomic profiling of a snake venom using high mass detection MALDI-TOF mass spectrometry

Oscar Yanes, Francesc X. Avilés, Ryan Wenzel, Alexis Nazabal, Renato Zenobi, Juan J. Calvete
2007 Journal of the American Society for Mass Spectrometry  
In this sense, MALDI-TOF mass spectrometry has partially replaced or complemented gel-based approaches for studying the proteomic profile of the low mass components of many complex biological samples such  ...  Most of the mass profiling studies performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) have been restricted to peptides and small proteins (Ͻ20 kDa  ...  OY acknowledges a fellowship from MCYT.  ... 
doi:10.1016/j.jasms.2006.11.007 pmid:17204429 fatcat:vgw5thzmlbc65knq3q6yoxqffe

NEW OPPORTUNITIES TO IDENTIFY AND TYPE STAPHYLOCOCCUS spp. BY USING MALDI-TOF MASS SPECTROMETRY

A. S. Stepanov, N. V. Vasilyeva
2019 Infekciâ i Immunitet  
Analysis of the median mass spectrometry profiles is recommended for Staphylococcus spp. intraspecific typing by using MALDI-TOF mass spectrometry as the most reproducible and consistent approach.  ...  As a result, two systems for MALDI-TOF mass spectrometry reliably identify Staphylococcus spp., but standardization of sample preparation and bioinformation analysis is required for Staphylococcus spp.  ...  Due to the libraries of MALDI-TOF mass spectrometers are separated, where is difficult to compare the effectiveness of MALDI-TOF mass spectrometry for the typing of Staphylococcus spp. and screening for  ... 
doi:10.15789/2220-7619-2018-4-489-496 fatcat:pvomj5drjfc25b3fayc43ln2hq

Rapid Identification of Intact Staphylococcal Bacteriophages Using Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry

Dana Štveráková, Ondrej Šedo, Martin Benešík, Zbyněk Zdráhal, Jiří Doškař, Roman Pantůček
2018 Viruses  
ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling that is among the suggested methods for meeting the regulations of pharmaceutical authorities.  ...  Phage tail and capsid proteins yielded the strongest signals whereas the culture conditions had no effect on mass spectral quality.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/v10040176 pmid:29617332 pmcid:PMC5923470 fatcat:f35dik6o7bgnhh4gkxtoh76bkm

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass-Spectrometry (MALDI-TOF MS) Based Typing of Extended-Spectrum β-Lactamase Producing E. coli – A Novel Tool for Real-Time Outbreak Investigation

Adrian Egli, Sarah Tschudin-Sutter, Michael Oberle, Daniel Goldenberger, Reno Frei, Andreas F. Widmer, Paul Proost
2015 PLoS ONE  
We compared six extended-spectrum β-lactamase producing E. coli of a PFGE-related cluster with Matrix-assisted laser desorption/ionization-time of flight mass-spectrometry based typing that confirmed relatedness  ...  faster and more cost-effective, but as reliable as PFGE.  ...  Acknowledgments We wish to thank Clarisse Straub, Magdalena Schneider, Elisabeth Schultheiss, and Sabrina Stammler (University Hospital Basel, Switzerland) for excellent technical assistance with the  ... 
doi:10.1371/journal.pone.0120624 pmid:25860943 pmcid:PMC4393243 fatcat:ienmqnp4gngpbaoez6rntjjulu

Screening of gluten avenins in foods by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Emilio Camafeita, Enrique Méndez
1998 Journal of Mass Spectrometry  
MALDI/TOF mass spectra of the ethanol extracts (100 mg mi-") from three different oat-containing food samples.  ...  Top: overlayed MALDI/TOF mass spectra of gliadins secalins and avenins (left) and mass profile expected in the ethanol extract from a food sample elaborated with a mixture of wheat (Senatore Capelli),  ... 
doi:10.1002/(sici)1096-9888(1998100)33:10<1023::aid-jms723>3.3.co;2-m pmid:9821333 fatcat:6znnh2h6cjayrgd44wav7jpzua

Screening of gluten avenins in foods by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Emilio Camafeita, Enrique Méndez
1998 Journal of Mass Spectrometry  
MALDI/TOF mass spectra of the ethanol extracts (100 mg mi-") from three different oat-containing food samples.  ...  Top: overlayed MALDI/TOF mass spectra of gliadins secalins and avenins (left) and mass profile expected in the ethanol extract from a food sample elaborated with a mixture of wheat (Senatore Capelli),  ... 
doi:10.1002/(sici)1096-9888(1998100)33:10<1023::aid-jms723>3.0.co;2-v pmid:9821333 fatcat:nlkkoiephfgtbcc6c2c37zp5au

The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4

Marek Šebela, Martin Raus, Vladan Ondřej, Petr Hašler
2021 Molecules  
The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp.  ...  laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).  ...  Protein extracts were made by treating cyanobacterial cells with the acidic matrix solvent to identify proteins for assigning the characteristic peaks in IC MALDI-TOF profiles: photosystem components,  ... 
doi:10.3390/molecules26061683 pmid:33802864 pmcid:PMC8002600 fatcat:3zgm7khlwnfuditwziqpcd2jkm

Characterization of Bacterial Lysates by Use of Matrix-Assisted Laser Desorption– Ionization Time of Flight Mass Spectrometry Fingerprinting

Norma Suárez, Ferrara F, Pirez M, Rial M, Chabalgoity A
2017 SOJ Biochemistry  
Here, we demonstrate that MALDI-TOF MS provides reliable and reproducible mass spectral fingerprints for bacterial lysates of S. pneumoniae, H. influenzae, K. pneumoniae, Staphylococcus spp.  ...  Overall, we found that mechanical lysis coupled to MS analysis allowed for accurate and highly sensible detection of key proteins in each bacterial lysate, a method that can be used to standardize batch-to-batch  ...  Arací Martínez for her technical assistance. We are indebted to Dr.Valerie Dee for her valuable revision of this work.  ... 
doi:10.15226/2376-4589/3/1/00124 fatcat:k5qfd6l2snczxfsaena3gdrx2y

MALDI-TOF-MS analysis in discovery and identification of serum proteomic patterns of ovarian cancer

Agata Swiatly, Agnieszka Horala, Joanna Hajduk, Jan Matysiak, Ewa Nowak-Markwitz, Zenon J. Kokot
2017 BMC Cancer  
Methods: Serum proteomic patterns in samples from OC patients were obtained using matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF).  ...  To broaden the knowledge on the pathological processes that occur during ovarian cancer tumorigenesis, protein-peptide profiling was proposed.  ...  The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1186/s12885-017-3467-2 pmid:28683725 pmcid:PMC5501370 fatcat:jpcu4uh4wzee3iulootczfd5gi

Identification of blood meal sources in the main African malaria mosquito vector by MALDI-TOF MS

Sirama Niare, Jean-Michel Berenger, Constentin Dieme, Ogobara Doumbo, Didier Raoult, Philippe Parola, Lionel Almeras
2016 Malaria Journal  
Moreover, using Aedes albopictus specimens, abdominal protein MS spectra from engorged mosquitoes were found specific to host blood source and independent of the mosquito species.  ...  A sequential analysis revealed stability of mosquito abdominal protein spectra up to 24 h post-feeding.  ...  Acknowledgements We thank Christophe Flaudrops (URMITE-IRD198, Marseille, France) for his advice on the analysis of MALDI-TOF MS profiles.  ... 
doi:10.1186/s12936-016-1152-6 pmid:26872451 pmcid:PMC4752743 fatcat:qmv2vnld75dxtiuchmk4w7tfku

Quantitative matrix-assisted laser desorption/ionization mass spectrometry

M. W. Duncan, H. Roder, S. W. Hunsucker
2008 Briefings in Functional Genomics & Proteomics  
This review summarizes the essential characteristics of matrix-assisted laser desorption/ionization (MALDI) timeof-flight mass spectrometry (TOF MS), especially as they relate to its applications in quantitative  ...  analysis.  ...  The combinatorial approach was devised to optimize the extraction by generating an array of solvent systems to be used for extraction from blood, and an automated analysis was performed by MALDI-TOF MS  ... 
doi:10.1093/bfgp/eln041 pmid:19106161 pmcid:PMC2722264 fatcat:742wmklqhzcntb7xoizuckhlem

MALDI-TOF MS as a new tool for the identification of Dientamoeba fragilis

Adriana Calderaro, Mirko Buttrini, Sara Montecchini, Sabina Rossi, Giovanna Piccolo, Maria Cristina Arcangeletti, Maria Cristina Medici, Carlo Chezzi, Flora De Conto
2018 Parasites & Vectors  
In this study for the first time, a Dientamoeba fragilis protein profile by MALDI-TOF MS was created in order to identify specific markers for the application of this technology in the laboratory diagnosis  ...  Conclusions: In our hands, MALDI-TOF MS technology was demonstrated as a useful tool to be used in association with or in replacement of the real-time PCR assay for the identification of D. fragilis used  ...  The datasets (raw data) used during the Fig. 4 Analysis of the spectra obtained from the two D. fragilis experimentally seeded fecal samples. a Example of discriminating peaks found in the fecal sample  ... 
doi:10.1186/s13071-017-2597-3 pmid:29301570 pmcid:PMC5755284 fatcat:x5slnczrhbdlxnnxphsnszuw2e

Matrix Assisted Laser Desorption Ionization-Time-of-Flight mass spectrometry identification of Mycobacterium bovis in Bovinae

Gisele BACANELLI, Larissa C. OLARTE, Márcio R. SILVA, Rudielle A. RODRIGUES, Paulo A.M. CARNEIRO, John B. KANEENE, Taynara N. PASQUATTI, Haruo TAKATANI, Martin J. ZUMÁRRAGA, Rodrigo N. ETGES, Flábio R. ARAÚJO, Newton V. VERBISCK
2019 Journal of Veterinary Medical Science  
For this purpose, the protein extraction protocol and the mass spectra reference database were optimized for the identification of 80 clinical isolates of mycobacteria.  ...  In this study, Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDI-TOF) mass spectrometry was used to identify Mycobacterium bovis from cattle and buffalo tissue isolates from the North and  ...  Daniel Sifuentes (analyst), from the Laboratory of Mass Spectrometry at Embrapa Genetic Resources and Biotechnology, by equipment usage support.  ... 
doi:10.1292/jvms.19-0214 pmid:31462609 pmcid:PMC6863732 fatcat:24evhvw3qrftjj74ivzss67rva

Tissue-specific signatures in tick cell line MS profiles

Dmitry S. Loginov, Yana F. Loginova, Filip Dycka, Katharina Böttinger, Pavlina Vechtova, Jan Sterba
2019 Parasites & Vectors  
For the first time, characteristic peaks in MS profiles of tick cell lines were assigned to proteins identified in acidic extracts of corresponding cell lines.  ...  A cell mass spectrometry approach (MALDI-TOF MS) was applied, as well as classical proteomic workflows.  ...  Acknowledgements We thank Dr Lesley Bell-Sakyi and the Tick Cell Biobank for provision of all tick cell lines, and Professor Ulrike Munderloh, University of Minnesota, for permission to use the IRE11,  ... 
doi:10.1186/s13071-019-3460-5 fatcat:r2c3wzykafcz3ao4fph7m4wnga
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