Use of SELDI-TOF mass spectrometry for identification of new biomarkers: potential and limitations

2007 ◽  
Vol 45 (11) ◽  
Author(s):  
Michael Kiehntopf ◽  
Robert Siegmund ◽  
Thomas Deufel
Keyword(s):  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Clinical Results ◽  
Protein Profiling ◽  
High Throughput Analysis ◽  
Pilot Studies ◽  
Flight Mass Spectrometry ◽  
Analytical Phase ◽  
New Biomarkers ◽  
Tof Ms

AbstractSurface-enhanced laser desorption time of flight mass spectrometry (SELDI-TOF-MS) is an important proteomic technology that is immediately available for the high throughput analysis of complex protein samples. Over the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis particularly with regard to the identification of novel biomarkers. Importantly, researchers have acquired a better understanding also of the limitations of this technology and various pitfalls in biomarker discovery. Bearing these in mind, great emphasis must be placed on the development of rigorous standards and quality control procedures for the pre-analytical as well as the analytical phase and subsequent bioinformatics applied to analysis of the data. To avoid the risk of false-significant results studies must be designed carefully and control groups accurately selected. In addition, appropriate tools, already established for analysis of highly complex microarray data, need to be applied to protein profiling data. To validate the significance of any candidate biomarker derived from pilot studies in appropriately designed prospective multi-center studies is mandatory; reproducibility of the clinical results must be shown over time and in different diagnostic settings. SELDI-TOF-MS-based studies that are in compliance with these requirements are now required; only a few have been published so far. In the meantime, further evaluation and optimization of both technique and marker validation strategies are called for before MS-based proteomic algorithms can be translated into routine laboratory testing.Clin Chem Lab Med 2007;45:1435–49.

scholarly journals APPLICATION OF TIME-OF-FLIGHT MASS-SPECTROMETRY FOR DETECTION OF CAUSATIVE AGENT OF BRUCELLOSIS IN BLOOD SAMPLES IN EXPERIMENT

2017 ◽  
pp. 9-17
Author(s):  
D. V. Ulshina ◽  
D. A. Kovalev ◽  
D. G. Ponomarenko ◽  
D. V. Rusanova ◽  
N. M. Shvetsova ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Causative Agent ◽  
Brucella Melitensis ◽  
Time Of Flight ◽  
Protein Profiling ◽  
Blood Samples ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Aim.Study the possibility to apply time-of-flight mass-spectrometry for detection of causative agent of brucellosis in blood. Materials and methods. Brucella strains: 5 Brucella melitensis and 21 Brucella abortus. Protein profiling in linear mode on MALD1-TOF mass-spectrometer Microflex «Bruker Daltonics». Results. Technique for disinfection and preparation of blood samples was modified and optimized for MALDI-TOF MS analysis. 120 representative protein profiles of sera extract were obtained that contain brucellosis causative agent. A resulting peak-list (super-spectrum) of the studied protein fraction of blood extract of a conditionally healthy human within the studied group was formed and analyzed. Conclusion. A scheme of brucella detection in blood samples by MALDI-TOF MS is proposed, based on detection of a complex of 15 genus-specific fragments. Signals on mass-spectra of extracts of leukocyte fraction of blood, artificially contaminated with brucellosis causative agents are characterized.

scholarly journals Population Genotyping of Hepatitis C Virus by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Analysis of Short DNA Fragments

2005 ◽  
Vol 51 (7) ◽  
pp. 1123-1131 ◽  
Author(s):  
Yoon Jun Kim ◽  
Soo-Ok Kim ◽  
Hyun Jae Chung ◽  
Mi Sun Jee ◽  
Byeong Gwan Kim ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Pcr Amplification ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Desorption Ionization ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

Abstract Background: Identifying hepatitis C virus (HCV) genotypes has become increasingly important for determining clinical course and the outcome of antiviral therapy. Here we describe the development of restriction fragment mass polymorphism (RFMP) analysis, a novel matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) assay suitable for high-throughput, sensitive, specific genotyping of multiple HCV species. Methods: The assay is based on PCR amplification and mass measurement of oligonucleotides containing genotype-specific motifs in the 5′ untranslated region, into which a type IIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products led to excision of multiple oligonucleotide fragments representing variable regions whose masses were determined by MALDI-TOF MS. Results: The RFMP assay identified viral genotypes present at concentrations as low as 0.5% and reliably determined their relative abundance. When sera from 318 patients were analyzed, the RFMP assay exhibited 100% concordance with results obtained by clonal sequencing and identified mixed-genotype infections in 22% of the samples, in addition to several subtype variants. Conclusions: The RFMP assay has practical advantages over existing methods, including better quantitative detection of mixed populations and detection of genotype variants without need for population-based cloning, enabling reliable viral genotyping in laboratories and efficient study of the relationship between viral genotypes and clinical outcome.

scholarly journals Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Is a Superior Diagnostic Tool for the Identification and Differentiation of Mycoplasmas Isolated from Animals

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Joachim Spergser ◽  
Claudia Hess ◽  
Igor Loncaric ◽  
Ana S. Ramírez
Keyword(s):  
Mass Spectrometry ◽  
Laser Desorption ◽  
Mycoplasma Species ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Desorption Ionization ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

ABSTRACTIn veterinary diagnostic laboratories, identification of mycoplasmas is achieved by demanding, cost-intensive, and time-consuming methods that rely on antigenic or genetic identification. Since matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) seems to represent a promising alternative to the currently practiced cumbersome diagnostics, we assessed its applicability for the identification of almost all mycoplasma species isolated from vertebrate animals so far. For generating main spectrum profiles (MSPs), the type strains of 98Mycoplasma, 11Acholeplasma, and 5Ureaplasmaspecies and, in the case of 69 species, 1 to 7 clinical isolates were used. To complete the database, 3 to 7 representatives of 23 undescribedMycoplasmaspecies isolated from livestock, companion animals, and wildlife were also analyzed. A large in-house library containing 530 MSPs was generated, and the diversity of spectra within a species was assessed by constructing dendrograms based on a similarity matrix. All strains of a given species formed cohesive clusters clearly distinct from all other species. In addition, phylogenetically closely related species also clustered closely but were separated accurately, indicating that the established database was highly robust, reproducible, and reliable. Further validation of the in-house mycoplasma library using 335 independent clinical isolates of 32 mycoplasma species confirmed the robustness of the established database by achieving reliable species identification with log scores of ≥1.80. In summary, MALDI-TOF MS proved to be an excellent method for the identification and differentiation of animal mycoplasmas, combining convenience, ease, speed, precision, and low running costs. Furthermore, this method is a powerful and supportive tool for the taxonomic resolution of animal mycoplasmas.

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