scholarly journals De novo sequencing of proteins and peptides: algorithms, applications, perspectives

2018 ◽  
Vol 1 (1) ◽  
pp. e00005 ◽  
Author(s):  
K.V. Vyatkina
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Database Search ◽  
Mass Spectrometric ◽  
Spectrometric Measurements ◽  
Further Development ◽  
Structure Of Proteins ◽  
Proteins And Peptides

Determination of the primary structure of proteins and peptides constitutes an important step in studying their properties. Currently, mass spectrometry is commonly applied to this end. The results of mass spectrometric measurements can be interpreted by means of either a database search or de novo sequencing methods. The appeal of the latter is due to their applicability to investigating unknown proteins, as well as the ones that cannot be analyzed with genomics or transcriptomics methods. In this paper, we briefly review the existing approaches to de novo sequencing of proteins and peptides, along with the problems that can be solved using those, and indicate directions and perspectives for their further development.

ON PREPROCESSING AND ANTISYMMETRY IN DE NOVO PEPTIDE SEQUENCING: IMPROVING EFFICIENCY AND ACCURACY

2008 ◽  
Vol 06 (03) ◽  
pp. 467-492 ◽  
Author(s):  
KANG NING ◽  
NAN YE ◽  
HON WAI LEONG
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Computational Models ◽  
De Novo ◽  
Noise Removal ◽  
Peptide Sequencing ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

Peptide sequencing plays a fundamental role in proteomics. Tandem mass spectrometry, being sensitive and efficient, is one of the most commonly used techniques in peptide sequencing. Many computational models and algorithms have been developed for peptide sequencing using tandem mass spectrometry. In this paper, we investigate general issues in de novo sequencing, and present results that can be used to improve current de novo sequencing algorithms. We propose a general preprocessing scheme that performs binning, pseudo-peak introduction, and noise removal, and present theoretical and experimental analyses on each of the components. Then, we study the antisymmetry problem and current assumptions related to it, and propose a more realistic way to handle the antisymmetry problem based on analysis of some datasets. We integrate our findings on preprocessing and the antisymmetry problem with some current models for peptide sequencing. Experimental results show that our findings help to improve accuracies for de novo sequencing.

scholarly journals Development, Optimization and Validation of a Sustainable and Quantifiable Methodology for the Determination of 2,4,6-Trichloroanisole, 2,3,4,6-Tetrachloroanisole, 2,4,6-Tribromoanisole, Pentachloroanisole, 2-Methylisoborneole and Geosmin in Air

Processes ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1571
Author(s):  
Patricia Jové ◽  
Marina Vives-Mestres ◽  
Raquel De Nadal ◽  
Maria Verdum
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
High Temperature ◽  
Thermal Desorption ◽  
Mass Spectrometric ◽  
Gas Chromatography Mass Spectrometry ◽  
Air Analysis ◽  
Good Linearity ◽  
Repeatability And Reproducibility

Compounds 2,4,6-trichloroanisole (TCA), 2,3,4,6-tetrachloroanisole (TeCA), 2,4,6-tribromoanisole (TBA) and pentachloroanisole (PCA), 2-methylisoborneol (2MIB) and geosmin (GSM) have been reported as being responsible for cork and wine taint. A sustainable method based on thermal desorption-gas chromatography–mass spectrometry (TD-GC/MS) has been developed and optimized, taking into account desorption parameters and chromatographic and mass spectrometric conditions. The combination of parameters that jointly maximized the compound detection was as follows: desorption temperature at 300 °C, desorption time at 30 min, cryo-temperature at 20 °C and trap high temperature at 305 °C. The proposed methodology showed a good linearity (R ≤ 0.994) within the tested range (from 0.1 to 2 ng) for all target compounds. The precision expressed as repeatability and reproducibility was RSD < 10% in both. The limits of quantification ranged from 0.05 to 0.1 ng. The developed methodology and the sampling rates (R-values) of all targeted compounds (from 0.013 to 0.071 m3 h−1) were applied to the air analysis of two wineries. The results showed that the developed methodology is a sustainable and useful tool for the determination of these compounds in air.

Mass Spectrometric Behaviour of Carboxylated Polyethylene Glycols and Carboxylated Octylphenol Ethoxylates

2003 ◽  
Vol 9 (3) ◽  
pp. 165-173 ◽  
Author(s):  
Magdalena Frańska ◽  
Agnieszka Zgoła ◽  
Joanna Rychłowska ◽  
Andrzej Szymański ◽  
Zenon Łukaszewski ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Alkali Metal ◽  
Mass Spectra ◽  
Secondary Ion Mass Spectrometry ◽  
Metal Cations ◽  
Mass Spectrometric ◽  
Polyethylene Glycols ◽  
Alkali Metal Cations ◽  
Secondary Ion

The mass spectrometric behaviour of mono- and di-carboxylated polyethylene glycols (PEGCs and CPEGCs) and carboxylated octylphenol ethoxylates (OPECs) is discussed. The tendency for ionisation (deprotonation, protonation and cationisation by alkali–metal cations) of carboxylated PEGs was compared with that of non-carboxylated analogues by using both secondary-ion mass spectrometry (SIMS) and electrospray ionisation (ESI). The fragmentation of the PEGCs and CPEGCs is discussed and also compared with their neutral analogues, PEGs. B/E linked-scan mass spectra were recorded, using secondary-ion mass spectrometry as a method for ion generation, for deprotonated and protonated molecules as well as for molecules cationised by alkali–metal cations. The fragmentation behaviour of PEGs is found to be different from that of CPEGCs, The presence of carboxyl groups may be confirmed not only by the determination of molecular weights of the ethoxylates studied, but also on the basis of the fragment ions formed. The metastable decomposition of the [OPEC-H]− ions proceeds through the cleavage of the bond between the octylphenol moiety and the ethoxylene chain and leads to the octylphenoxyl anions. It permits determination of the mass of the hydrophobic moiety of the studied carboxylated alkylphenol ethoxylate. ESI mass spectra recorded in the negative-ion mode were found to be more suitable than SI mass spectra for the determination of the average molecular weight of carboxylated ethoxylates.

Gas Chromatographic/Mass Spectrometric Determination of α-Methylstyrene in Styrene-Based Polymers and Food Simulants

1991 ◽  
Vol 74 (5) ◽  
pp. 815-818
Author(s):  
Shigeru Tan ◽  
Takashi Tatsuno ◽  
Taro Okada
Keyword(s):  
Mass Spectrometry ◽  
Direct Injection ◽  
Mass Spectrometric ◽  
Gas Chromatography Mass Spectrometry ◽  
Selected Ion Monitoring ◽  
Monitoring Method ◽  
Food Simulants ◽  
Multiple Ion Monitoring ◽  
Chromatographic Mass

Abstract A selected ion monitoring method is described for the analysis of styrene (St)-based polymers for a-methylstyrene (α- MSt) and for determining the level of α-MSt migration from St-based sheets Into 4 food simulants. The polymers are dissolved in dlchloromethane; α-MSt Is determined by direct Injection of the polymer solutions. α-MSt migration from St-based sheet to water, 4% acetic acid, 20% ethanol, and n-heptane was measured by gas chromatography/mass spectrometry, using multiple ion monitoring of Ions at mix 118,78, and 91. α-MSt can be quantltated at levels as low as 10 μ/g in the polymer and 0.01 μ/g In the food simulants. Recoveries were 83-113% from St-based sheets and 90-99% from food simulants, respectively.

Mass spectral analysis of acetylated peptides: Implications in proteomics

2019 ◽  
Vol 26 (1) ◽  
pp. 36-45
Author(s):  
Deepika Chandra ◽  
P Gayathri ◽  
Mudita Vats ◽  
R Nagaraj ◽  
MK Ray ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Pseudomonas Syringae ◽  
Mass Spectra ◽  
De Novo ◽  
Spectral Quality ◽  
Tryptic Peptides ◽  
Mass Spectral ◽  
Human Proteins ◽  
Terminal Amino

Sequence determination of peptides using mass spectrometry plays a crucial role in the bottom-up approaches for the identification of proteins. It is crucially important to minimise false detection and validate sequence of the peptides in order to correctly identify a protein. Chemical modification of peptides followed by mass spectrometry is an option for improving the spectral quality. In silico-derived tryptic peptides with different N-terminal amino acids were designed from human proteins and synthesized. The effect of acetylation on the fragmentation of peptides was studied. N-terminal acetylation of the tryptic peptides was shown to form b1-ions, improve the abundance and occurrence of b-ions. In some cases, the intensity and occurrence of some y-ions also varied. Thus, it is demonstrated that acetylation plays an important role in improving the de novo sequencing efficiency of the peptides. The acetylation method was extended to tryptic peptides generated from the proteome of an Antarctic bacterium Pseudomonas syringae Lz4W using the proteomics work flow and mass spectra of the peptides were analysed. Comparison of the MS/MS spectra of the acetylated and unacetylated peptides revealed that acetylation helped in improving the spectral quality and validated the peptide sequences. Using this method, 673 proteins of the 1070 proteins identified were validated.

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