Automated MALDI-TOF-MS Sample Preparation in Combinatorial Polymer Research

Abstract Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is now used as a routine technique for the fast and reliable identification of fungi at the species level and, currently, it represents an important phenotypic methodology based on proteomic profiles. The main limitations to MALDI-TOF MS for fungal identification are related to sample quality (e.g. quality of biological material such as rigidity or pigmentation of cell walls), sample preparation (e.g. the myriad of sample preparation methodologies that deliver different data sets to different MALDI-TOF MS databases) and the databases themselves (e.g. the 'black-box' commercial databases). This chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed.

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Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex

Molecules ◽

10.3390/molecules25143214 ◽

2020 ◽

Vol 25 (14) ◽

pp. 3214

Author(s):

Gabor Maasz ◽

Zita Zrínyi ◽

Istvan Fodor ◽

Nóra Boross ◽

Zoltán Vitál ◽

...

Keyword(s):

Sample Preparation ◽

Cryptic Species ◽

Species Complex ◽

Intraspecific Variability ◽

Clove Oil ◽

Term Survival ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Ms Analysis ◽

Tof Ms

Knowledge of intraspecific variability of a certain species is essential for their long-term survival and for the development of conservation plans. Nowadays, molecular/genetic methods are the most frequently used for this purpose. Although, the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) technique has become a promising alternative tool to specify intraspecific variability, there is a lack of information about the limitations of this method, and some methodological issues need to be resolved. Towards this goal, we tested the sensitivity of this method on an intraspecific level, using genetically identified individuals of a cryptic fish species complex collected from five distinct populations. Additionally, some methodologic issues, such as the effect of (1) delayed sample preparation, (2) clove oil anaesthetization, and (3) different tissue types (muscle, and brain) were investigated using the MS analysis results. Our results show that the delayed sample preparation has a fundamental effect on the result of MS analysis, while at the same time the clove oil did not affect the results considerably. Both the brain and muscle samples were usable for cryptic species identification, but in our opinion this method has limited applicability for population-level segregation. The application of MALDI-TOF MS to the exploitable toolkit of phylogenetic and taxonomic researches could be used to broaden conclusions.

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MALDI-TOF MS-Based Analysis of Seed Proteins from Catalogue Varieties of Solanum lycopersicum/Lycopersicon esculentum

Horticulturae ◽

10.3390/horticulturae5030048 ◽

2019 ◽

Vol 5 (3) ◽

pp. 48

Author(s):

Michael Reeve

Keyword(s):

Lycopersicon Esculentum ◽

Sample Preparation ◽

Solanum Lycopersicum ◽

Seed Proteins ◽

Impatiens Glandulifera ◽

Invasive Weed ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Commercial Plant ◽

Tof Ms

Matrix-assisted laser-desorption and ionization time-of-flight mass spectroscopy (MALDI-TOF MS) is a flexible technique for the analysis of protein-containing biological samples. Simple and inexpensive methods have previously been developed for MALDI-TOF MS sample preparation that are able to discriminate between Impatiens species that are closely related and also between regional biotypes of the invasive weed Impatiens glandulifera (Himalayan balsam) with leaf material and also seed material. The current article investigates whether MALDI-TOF MS, through acid-soluble protein ‘fingerprinting’, can be used to analyze plant seeds that result from intensive commercial plant-breeding activity. As an initial proof-of-concept study, tomato seeds from eleven seed-catalogue varieties (F1 Pink Baby Plum, F1 Fantasio, F1 Lizzano, F1 Sungold, F1 Tumbler, Faworyt, Golden Sunrise, Hundreds and Thousands, Indigo Rose, Moneymaker, and Red Alert), listed as Solanum lycopersicum or under the synonym Lycopersicon esculentum were analyzed using MALDI-TOF MS. Whilst peak-rich and highly-reproducible spectra were obtained, with very high Bruker comparison scores and low MALDI-TOF MS variance, sample-preparation variance, and seed-to-seed variance, the spectral differences between varieties were only slightly greater than the above combined variances, indicating very close similarity between all eleven varieties studied. These results are discussed in comparison with those previously observed with the naturally-evolving invasive species I. glandulifera.

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Direct analysis of positive blood cultures using MALDI-TOF MS profiling and a fundamentally improved sample preparation technique

Pathology ◽

10.1016/s0031-3025(16)33250-0 ◽

2011 ◽

Vol 43 ◽

pp. S73-S74

Author(s):

Guido Mix ◽

Leith Fremlin ◽

Thomas Maier ◽

Beatrix Wegemann ◽

Markus Kostrzewa

Keyword(s):

Sample Preparation ◽

Direct Analysis ◽

Blood Cultures ◽

Preparation Technique ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Sample Preparation Technique ◽

Tof Ms

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Profiling embryonic stem cell differentiation by MALDI-MS: development of a reproducible and robust sample preparation workflow

10.1101/536664 ◽

2019 ◽

Author(s):

Rachel E. Heap ◽

Anna Segarra-Fas ◽

Greg M. Findlay ◽

Matthias Trost

Keyword(s):

Sample Preparation ◽

Mammalian Cell ◽

Mammalian Cells ◽

Embryonic Stem ◽

Stem Cell Differentiation ◽

Embryonic Stem Cell Differentiation ◽

Maximum Information ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Tof Ms

ABSTRACTMALDI-TOF mass spectrometry (MS) is widely used to characterize and biotype bacterial samples, but a complimentary method for profiling of mammalian cells is still underdeveloped. Current approaches vary dramatically in their sample preparation methods and are not suitable for high-throughput studies. In this work, we present a universal workflow for mammalian cell MALDI-TOF MS analysis and apply it to distinguish ground-state naïve and differentiating mouse embryonic stem cells (mESCs), which can be used as a model for drug discovery. We employed a systematic approach testing many parameters to evaluate how efficiently and reproducibly each method extracted unique mass features from four different human cell lines. This data enabled us to develop a unique mammalian cell MALDI-TOF workflow involving a freeze-thaw cycle, methanol fixing and CHCA matrix to generate spectra that yield maximum information and are highly reproducible. We applied our optimized workflow to distinguish naïve and differentiating populations using multivariate analysis and reproducibly identifying unique features. Consequently, our MALDI-TOF MS profiling method enables identification of unique biomarkers and robust phenotyping of mESC differentiation. This method can in the future be applied to profile other cell types and expanded towards cellular MALDI-TOF MS screening assays.

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Sample preparation and culture condition effects on MALDI‐TOF MS identification of bacteria: A review

Mass Spectrometry Reviews ◽

10.1002/mas.21739 ◽

2021 ◽

Author(s):

Natalija Topić Popović ◽

Snježana P. Kazazić ◽

Krunoslav Bojanić ◽

Ivančica Strunjak‐Perović ◽

Rozelindra Čož‐Rakovac

Keyword(s):

Sample Preparation ◽

Culture Condition ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Identification Of Bacteria ◽

Tof Ms

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Toward Prediction: Using Chemometrics for the Optimization of Sample Preparation in MALDI-TOF MS of Synthetic Polymers

Analytical Chemistry ◽

10.1021/ac101526w ◽

2010 ◽

Vol 82 (19) ◽

pp. 8169-8175 ◽

Cited By ~ 16

Author(s):

Heike Brandt ◽

Thomas Ehmann ◽

Matthias Otto

Keyword(s):

Sample Preparation ◽

Synthetic Polymers ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Tof Ms

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Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi

Medical Mycology ◽

10.1093/mmy/myaa037 ◽

2020 ◽

Vol 59 (1) ◽

pp. 81-86

Author(s):

Yue Sun ◽

Jian Guo ◽

Rong Chen ◽

Liang Hu ◽

Qihang Xia ◽

...

Keyword(s):

Sample Preparation ◽

Filamentous Fungi ◽

Reference Method ◽

Species Level ◽

Its Sequencing ◽

Maldi Tof Ms ◽

Genus Level ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Tof Ms

Abstract Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.

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Hexagonal Mesoporous Silica as a Rapid, Efficient and Versatile Tool for MALDI-TOF MS Sample Preparation in Clinical Peptidomics Analysis: A Pilot Study

Molecules ◽

10.3390/molecules24122311 ◽

2019 ◽

Vol 24 (12) ◽

pp. 2311

Author(s):

Rosa Terracciano ◽

Mariaimmacolata Preianò ◽

Giuseppina Maggisano ◽

Corrado Pelaia ◽

Rocco Savino

Keyword(s):

Synovial Fluid ◽

Mesoporous Silica ◽

Sample Preparation ◽

Solid Phase ◽

Phase Extraction ◽

Dispersive Solid Phase Extraction ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Versatile Tool ◽

Tof Ms

Improvement in high-throughput MALDI-TOF MS analysis requires practical and efficient sample preparation protocols for high acquisition rates. The use of hexagonal mesoporous silica (HMS) sorbents in combination with MALDI-TOF MS was explored as a versatile tool for peptidomic profiling of clinical specimens difficult to process, but considered important sources of disease biomarkers: synovial fluid and sputum. A rapid and efficient procedure, based on dispersive solid-phase extraction of peptides using commercially available wormhole mesostructured HMS, was tested for: a) pre-concentration of standard peptides in serially diluted solution up to the sub-nanomolar range; b) peptidome profiling of sputum and synovial fluid. The use of HMS, as dispersed sponges, significantly amplified the peptidic repertoire of sputum and synovial fluid by excluding from the adsorptive process large size proteins, which mask and/or suppress peptidome signals. The protocol proposed, as dispersive solid phase extraction, ensures good analytical performances. Moreover, it is economical and rapid, as it avoids the use of less reproducible and prolonged sample preparation procedures, such as the use of ultrafiltration filter devices. These findings may contribute to defining a high-throughput screening MS-based platform for monitoring key peptidic features of difficult to analyse bodily fluids in a clinical setting.

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