Single Peptide-Based Protein Identification in Human Proteome through MALDI-TOF MS Coupled with Amino Acids Coded Mass Tagging

2003 ◽  
Vol 75 (6) ◽  
pp. 1316-1324 ◽  
Author(s):  
Songqin Pan ◽  
Sheng Gu ◽  
E. Morton Bradbury ◽  
Xian Chen
Keyword(s):  
Amino Acids ◽  
Protein Identification ◽  
Human Proteome ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Single Peptide ◽  
Tof Ms

scholarly journals Detection of Structural and Conformational Changes in ALS-Causing Mutant Profilin1 With Hydrogen/Deuterium Exchange Mass Spectrometry and Bioinformatics Techniques

2021 ◽  
Author(s):  
Ahmad Shahir Sadr ◽  
zahra abdollahpour ◽  
Atousa Aliahmadi ◽  
Changiz Eslahchi ◽  
Mina Nekouei ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Amino Acid ◽  
Conformational Changes ◽  
Docking Simulation ◽  
Hydrogen Deuterium Exchange ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Hydrogen Deuterium ◽  
Tof Ms

Abstract The hydrogen/deuterium exchange (HDX) is a reliable method to survey the dynamic behavior of proteins and epitope mapping. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a quantifying tool to assay for HDX in the protein of interest. We combined HDX-MALDI-TOF MS and molecular docking/MD simulation to identify accessible amino acids and analyze their contribution in the structural changes of profilin1 (PFN1). The molecular docking/MD simulations are computational tools for enabling the analysis of the type of amino acids that may be involved via HDX identified under the lowest binding energy condition. Glycine to Valine amino acid (G117V) substitution mutation is linked to amyotrophic lateral sclerosis (ALS). This mutation is found to be in the actin-binding site of PFN1 and prevents the dimerization/polymerization of actin and invokes a pathologic toxicity that leads to ALS. In this study, we sought to understand the PFN1 protein dynamic behavior using purified wild type and mutant PFN1 proteins. The data obtained from HDX-MALDI-TOF MS for PFN1WT and PFN1G117V at various time intervals, from seconds to hours, revealed multiple peaks corresponding to molecular weights from monomers to multimers. PFN1/Benzaldehyde complexes identified 20 accessible amino acids to HDX that participate in the docking simulation in the surface of WT and mutant PFN1. Consistent results from HDX-MALDI-TOF MS and docking simulation predict candidate amino acid(s) involved in the dimerization/polymerization of PFNG117V. This information may shed critical light on the structural and conformational changes with details of amino acid epitopes for mutant PFN1s’ dimerization, oligomerization, and aggregation.

A Microsystem Platform Interfacing MALDI-TOF MS for High Speed Automated Protein Identification

2000 ◽  
pp. 455-458 ◽  
Author(s):  
Simon Ekström ◽  
Patrik Önnerfjord ◽  
Martin Bengtsson ◽  
Tasso Miliotis ◽  
David Ericsson ◽  
...  
Keyword(s):  
High Speed ◽  
Protein Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Age-Related Homeostasis: Molecular Mechanism, Disease and Predictions from Global Analyses of Mouse Liver Proteins.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1611-1611
Author(s):  
Sumiko Kurachi ◽  
Taku Tanaka ◽  
Muneyoshi Kanai ◽  
Emi Suenaga ◽  
Elena Solovieva ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Protein Identification ◽  
Molecular Mechanisms ◽  
Nuclear Protein ◽  
Hemophilia B ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Age Related ◽  
Puberty Onset ◽  
Tof Ms

Abstract We previously reported the first molecular mechanism underlying the age-related homeostasis, ASE/AIE-mediated genetic mechanism for age-related regulation of gene expression, which turned out to be a mechanism of puberty-onset gene switching, specifically controlling a group of genes for their expression from puberty into old age (Kurachi & Kurachi J Thromb Haemost 2005; Zahng et al J Biol Chem277:4532, 2002; Kurachi et al Science285:739, 1999). This led us to successful construction of a transgenic mouse model of hemophilia B Leyden, a unique subset of hemophilia B with its mechanism being remained mysterious, robustly mimicking its unusual pattern of puberty-onset spontaneous amelioration. With this background, we hypothesized that besides the ASE/AIE-mediated mechanism, there exist more unidentified fundamental regulatory mechanisms for age-related homeostasis, which individually or in various combinations generate age-related complex and dynamic regulatory patterns of liver proteins. We launched a series of global and quantitative analysis of age-related changes in expression of liver nuclear proteins of mice (C57BL/6xSJL, [male], 1 through-24 month of age) by taking a procedure composed of two-dimensional gel electrophoresis (2DE) for separation and quantification of liver nuclear protein spots and of MALDI-TOF/MS PMF analyses to identify proteins in the spots. Out of over 6000 spots recognized and quantified in 2DE, 4547 protein spots were subjected to MALDI-TOF/MS analysis for protein identification. Finally, 2765 protein spots including many isomers were found unique. Systematic analyses of their age-related expression identified several major phases in protein expression throughout the lifespan. These findings supported our hypothesis that there exist multiple novel molecular mechanisms responsible for maintaining age-related homeostasis. The comprehensive liver nuclear protein data set was then used to construct a comprehensive database, which allows rapid and reliable searches for expression of specific proteins, their age-related dynamic profiles, isomers, protein identification from 2DE image, and other related information. This will serve as a valuable platform resource for studying epigenetic challenges, evaluation of drugs as well as gaining further insights into the molecular mechanisms underlying age-related homeostasis.

Core–Shell Gold Nanoparticles as Non-Conventional Matrix for the MALDI-ToF-MS Detection of Amino Acids: A Preliminary Study

2008 ◽  
Vol 6 (4) ◽  
pp. 654-661 ◽  
Author(s):  
N. Cioffi ◽  
F. De Palo ◽  
C. D. Calvano ◽  
I. D. van der Werf ◽  
F. Palmisano ◽  
...  
Keyword(s):  
Amino Acids ◽  
Gold Nanoparticles ◽  
Core Shell ◽  
Maldi Tof Ms ◽  
Ms Detection ◽  
Maldi Tof ◽  
Preliminary Study ◽  
Tof Ms

Protein Identification by MALDI-TOF-MS Peptide Mapping:  A New Strategy

2002 ◽  
Vol 74 (8) ◽  
pp. 1760-1771 ◽  
Author(s):  
Volker Egelhofer ◽  
Johan Gobom ◽  
Harald Seitz ◽  
Patrick Giavalisco ◽  
Hans Lehrach ◽  
...  
Keyword(s):  
Protein Identification ◽  
Peptide Mapping ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
New Strategy ◽  
Tof Ms

scholarly journals Low doses of Bisphenol S affect post-translational modifications of sperm proteins in male mice

2020 ◽  
Author(s):  
Hedvika Řimnáčová ◽  
Miriam Štiavnická ◽  
Jiří Moravec ◽  
Marouane Chemek ◽  
Yaroslav Kolinko ◽  
...  
Keyword(s):  
Protein Identification ◽  
Testicular Tissue ◽  
Low Doses ◽  
Male Mice ◽  
Bisphenol S ◽  
Experimental Conditions ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Sperm Proteins ◽  
Tof Ms

Abstract Background: Bisphenol S (BPS) is increasingly used as a replacement for bisphenol A in the manufacture of products containing polycarbonates and epoxy resins. However, further studies of BPS exposure are needed for the assessment of health risks to humans. In this study we assessed the potential harmfulness of low-dose BPS on reproduction in male mice.Methods: To simulate human exposure under experimental conditions, 8-week-old outbred ICR male mice received 8 weeks of drinking water containing a broad range of BPS doses [0.001, 1.0, or 100 µg/kg body weight (bw)/day, BPS1-3] or vehicle control. Mice were sacrificed and testicular tissue taken for histological analysis and protein identification by nano-liquid chromatography/mass spectrometry (MS) and sperm collected for immunodetection of acetylated lysine and phosphorylated tyrosine followed by protein characterisation using matrix-assisted laser desorption ionisation time-of-flight MS (MALDI-TOF MS).Results: The results indicate that compared to vehicle, 100 µg/kg/day exposure (BPS3) leads to 1) significant histopathology in testicular tissue; and, 2) higher levels of the histone protein γH2AX, a reliable marker of DNA damage. There were fewer mature spermatozoa in the germ layer in the experimental group treated with 1 µg/kg bw (BPS2). Finally, western blot and MALDI-TOF MS studies showed significant alterations in the sperm acetylome and phosphorylome in mice treated with the lowest exposure (0.001 µg/kg/day; BPS1), although the dose is several times lower than what has been published so far. Conclusions: In summary, this range of qualitative and quantitative findings in young male mice raise the possibility that very low doses of BPS may impair mammalian reproduction through epigenetic modifications of sperm proteins.

scholarly journals Low doses of Bisphenol S affect post-translational modifications of sperm proteins in male mice

2020 ◽  
Author(s):  
Hedvika Řimnáčová ◽  
Miriam Štiavnická ◽  
Jiří Moravec ◽  
Marouane Chemek ◽  
Yaroslav Kolinko ◽  
...  
Keyword(s):  
Protein Identification ◽  
Testicular Tissue ◽  
Low Doses ◽  
Male Mice ◽  
Bisphenol S ◽  
Experimental Conditions ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Sperm Proteins ◽  
Tof Ms

Abstract Background: Bisphenol S (BPS) is increasingly used as a replacement for bisphenol A in the manufacture of products containing polycarbonates and epoxy resins. However, further studies of BPS exposure are needed for the assessment of health risks to humans. In this study we assessed the potential harmfulness of low-dose BPS on reproduction in male mice.Methods: To simulate human exposure under experimental conditions, 8-week-old outbred ICR male mice received 8 weeks of drinking water containing a broad range of BPS doses [0.001, 1.0, or 100 µg/kg body weight (bw)/day, BPS1-3] or vehicle control. Mice were sacrificed and testicular tissue taken for histological analysis and protein identification by nano-liquid chromatography/mass spectrometry (MS) and sperm collected for immunodetection of acetylated lysine and phosphorylated tyrosine followed by protein characterisation using matrix-assisted laser desorption ionisation time-of-flight MS (MALDI-TOF MS).Results: The results indicate that compared to vehicle, 100 µg/kg/day exposure (BPS3) leads to 1) significant histopathology in testicular tissue; and, 2) higher levels of the histone protein γH2AX, a reliable marker of DNA damage. There were fewer mature spermatozoa in the germ layer in the experimental group treated with 1 µg/kg bw (BPS2). Finally, Western blot and MALDI-TOF MS studies showed significant alterations in the sperm acetylome and phosphorylome in mice treated with the lowest (BPS1) exposure (0.001 µg/kg/day).Conclusions: In summary, this range of qualitative and quantitative findings in young male mice raise the possibility that relatively low doses of BPS may impair mammalian reproduction through epigenetic modifications of sperm proteins.

scholarly journals Low doses of Bisphenol S affect post-translational modifications of sperm proteins in male mice

2020 ◽  
Author(s):  
Hedvika Řimnáčová ◽  
Miriam Štiavnická ◽  
Jiří Moravec ◽  
Marouane Chemek ◽  
Yaroslav Kolinko ◽  
...  
Keyword(s):  
Protein Identification ◽  
Testicular Tissue ◽  
Low Doses ◽  
Male Mice ◽  
Bisphenol S ◽  
Experimental Conditions ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Sperm Proteins ◽  
Tof Ms

Abstract Background Bisphenol S (BPS) is increasingly used as a replacement for bisphenol A in the manufacture of products containing polycarbonates and epoxy resins. However, further studies of BPS exposure are needed for the assessment of health risks to humans. In this study we assessed the potential harmfulness of low-dose BPS on reproduction in male mice. Methods To simulate human exposure under experimental conditions, 8-week-old outbred ICR male mice received 8 weeks of drinking water containing a broad range of BPS doses [0.001, 1.0, or 100 µg/kg body weight (bw)/day, BPS1-3] or vehicle control. Mice were sacrificed and testicular tissue taken for histological analysis and protein identification by nano-liquid chromatography/mass spectrometry (MS) and sperm collected for immunodetection of acetylated lysine and phosphorylated tyrosine followed by protein characterisation using matrix-assisted laser desorption ionisation time-of-flight MS (MALDI-TOF MS). Results The results indicate that compared to vehicle, 100 µg/kg/day exposure (BPS3) leads to 1) significant histopathology in testicular tissue; and, 2) higher levels of the histone protein γH2AX, a reliable marker of DNA damage. There were fewer mature spermatozoa in the germ layer in the experimental group treated with 1 µg/kg bw (BPS2). Finally, Western blot and MALDI-TOF MS studies showed significant alterations in the sperm acetylome and phosphorylome in mice treated with the lowest (BPS1) exposure (0.001 µg/kg/day). Conclusions In summary, this range of qualitative and quantitative findings in young male mice raise the possibility that relatively low doses of BPS may impair mammalian reproduction through epigenetic modifications of sperm proteins.

Proteomic assessment of an established technique for carboxysome enrichment from Synechococcus PCC7942

2005 ◽  
Vol 83 (7) ◽  
pp. 746-757 ◽  
Author(s):  
Ben M Long ◽  
G Dean Price ◽  
Murray R Badger
Keyword(s):  
Protein Identification ◽  
Bisphosphate Carboxylase ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Enrichment Technique ◽  
Concentrating Mechanism ◽  
Key Enzyme ◽  
Synechococcus Pcc7942 ◽  
Tof Ms

Carboxysomes are protein-bound, polyhedral microbodies within cyanobacteria, containing the key enzyme for photosynthetic CO2 fixation, ribulose-1,5-bisphosphate carboxylase–oxygenase (Rubisco). Sequencing of cyanobacterial genomes has revealed that cyanobacteria possess one or other of two types of carboxysomes. Cyanobacteria containing form 1A Rubisco possess α-carboxysomes, while those with form 1B Rubisco possess β-carboxysomes. Given the central importance of carboxysomes in the CO2-concentrating mechanism of cyanobacteria, understanding the nature and composition of these structures is of considerable importance. In an effort to develop techniques for the characterization of the structure of β-carboxysomes, particularly the outer protein shell, we have undertaken a proteomic assessment of the Percoll–Mg2+ carboxysome enrichment technique using the freshwater cyanobacterium Synechococcus sp. PCC7942. Both matrix-assisted laser desorption–ionization – time of flight mass spectrometry (MALDI-TOF MS) and multidimensional protein identification technology (MuDPIT) methods were used to determine the protein content of a novel carboxysome-rich fraction. A total of 17 proteins were identified using MALDI-TOF MS from enriched carboxysome preparations, while 122 proteins were identified using MuDPIT analysis on the same material. The carboxysomal protein CcmM was identified by MALDI-TOF MS as two distinct proteins of 38 and 58 kDa. The only other carboxysomal proteins identified were the large and small subunits of Rubisco (RbcL and RbcS). Reasons for the lack of evidence for the expected full complement of carboxysomal proteins and future directions are discussed.Key words: CO2-concentrating mechanism, cyanobacteria, carboxysomes, proteomics.

Improvements in Protein Identification by MALDI-TOF-MS Peptide Mapping

2000 ◽  
Vol 72 (13) ◽  
pp. 2741-2750 ◽  
Author(s):  
Volker Egelhofer ◽  
Konrad Büssow ◽  
Christine Luebbert ◽  
Hans Lehrach ◽  
Eckhard Nordhoff
Keyword(s):  
Protein Identification ◽  
Peptide Mapping ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms
Sign in / Sign up

Export Citation Format

Share Document