MALDI-TOF characterization of NAPPA-generated proteins

Spera, Rosanna; LaBaer, Joshua; Nicolini, Claudio

doi:10.1002/jms.1976

Cited by 20 publications

(28 citation statements)

References 9 publications

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“…The databank search of samples in the experimental mass lists obtained by MALDI-TOF or LC-ESI-MS provided the identification, with significant scores, of molecules of MM or E. coli lysate (Figure 4). Different strategies have been addressed to overcome the presence of these "background" molecules that represented [29]. By pursuing the coupling of our newly developed software SpADS to K Means Cluster algorithm we obtained good results both for known and unknown protein identification, up to 67% correct score, quite better than earlier MS without SNAP.…”

Section: Determination Of Protein-protein Interaction For Cancer Contmentioning

confidence: 98%

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Nicolini¹,

Bragazzi²,

Pechkova³

2015

NanoWorld J

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Section: Determination Of Protein-protein Interaction For Cancer Contmentioning

confidence: 98%

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Nicolini¹,

Bragazzi²,

Pechkova³

2015

NanoWorld J

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“…Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) allows the sensitive analysis of hundreds of different molecules in a single experiment. Therefore, it has been applied in the screening of protein microarrays to characterize proteins and analyze the binding between proteins and other molecules [19][20][21]. However, it is well known that the selection of matrix in MALDI experiments impacts the results.…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Screening of the Binding of Small Molecules to Proteins by Desorption Electrospray Ionization Mass Spectrometry Combined with Protein Microarray

Yao

Wang

Zhang

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. The interaction between bioactive small molecule ligands and proteins is one of the important research areas in proteomics. Herein, a simple and rapid method is established to screen small ligands that bind to proteins. We designed an agarose slide to immobilize different proteins. The protein microarrays were allowed to interact with different small ligands, and after washing, the microarrays were screened by desorption electrospray ionization mass spectrometry (DESI MS). This method can be applied to screen specific protein binding ligands and was shown for seven proteins and 34 known ligands for these proteins. In addition, a high-throughput screening was achieved, with the analysis requiring approximately 4 s for one sample spot. We then applied this method to determine the binding between the important protein matrix metalloproteinase-9 (MMP-9) and 88 small compounds. The molecular docking results confirmed the MS results, demonstrating that this method is suitable for the rapid and accurate screening of ligands binding to proteins.

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“…[3]; the labeled molecule is then detected via a fluorescence microscope, flow cytometer or some other fluorescence reading instrument [4]. On the contrary label-free analysis do not require the use of reporter elements (fluorescent, luminescent, radiometric, or colorimetric) to facilitate measurements, it can provide direct information on analyte binding to array molecules typically in the form of mass addition or depletion from the array surface [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

“…Many label-free techniques such as SPR, quartz crystal microbalance (QCM), carbon nanotubes (CNTs) and nanowires, nanohole arrays, atomic force microscopy (AFM), etc., have been successfully integrated with protein microarrays and are emerging rapidly as a potential TOF MS analysis of Nucleic Acid Programmable Protein Array (NAPPA) [5]. The NAPPA method allows for functional proteins to be synthesized in situ directly from printed cDNAs just in time for assay [10,11].…”

Section: Introductionmentioning

confidence: 99%

Mass Spectrometry and Florescence Analysis of Snap-Nappa Arrays Expressed Using E. coli Cell_Free Expression System

Nicolini

Spera

Festa³

et al. 2013

J Nanomed Nanotechnol

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We present the analysis of an innovative kind of self-assembling protein microarray, the "Nucleic Acid Programmable Protein Array" (NAPPA), express with the SNAP tag in E.coli coupled self free expression system. The goal is to develop a standardize procedure to analyze the protein protein interaction occurred on NAPPA array combining label free Mass Spectrometry (MS) and fluorescence technology for protein microarray. We employ in the process "Protein synthesis Using Recombinant Elements" (PURE) system. For the first time an improved version of NAPPA, that allows for functional proteins to be synthesized in situ -with a SNAP tag -directly from printed cDNAs just in time for assay, has been expressed with a novel cell-free transcription/translation system reconstituted from the purified components necessary for Escherichia coli translation -the PURE system -and analyzed both in fluorescence and in a label free manner by four different mass spectrometers, namely three Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF), a Voyager, a Bru ker Autoflex and a Bruker Ultraflex, and Liquid Chromatography-Electrospray Ionization Mass Spectrometry (LC-ESI-MS/MS). Due to the high complexity of the system, an ad hoc bioinformatic tool has been needed to develop for their successful analysis. The contemporary fluorescence analysis of NAPPA, expressed by means of PURE system, has been performed to confirm the improved characterization of this new NAPPA-SNAP system.

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MALDI-TOF characterization of NAPPA-generated proteins

Cited by 20 publications

References 9 publications

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Screening of the Binding of Small Molecules to Proteins by Desorption Electrospray Ionization Mass Spectrometry Combined with Protein Microarray

Mass Spectrometry and Florescence Analysis of Snap-Nappa Arrays Expressed Using E. coli Cell_Free Expression System

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