scholarly journals De novo Sequencing and Native Mass Spectrometry Reveals Hetero-Association of Dirigent Protein Homologs and Potential Interacting Proteins in Forsythia × intermedia

The Analyst ◽  
2021 ◽  
Author(s):  
Mowei Zhou ◽  
Joseph A Laureanti ◽  
Callum Bell ◽  
Mi Kwon ◽  
Qingyan Meng ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Native Mass Spectrometry ◽  
De Novo Sequencing ◽  
Interacting Proteins ◽  
Dirigent Protein ◽  
Radical Coupling ◽  
Dirigent Proteins

The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro...

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.

Shotgun Sequencing Small Oligonucleotides by Nozzle-Skimmer Dissociation and Electrospray Ionization Mass Spectrometry

2005 ◽  
Vol 11 (2) ◽  
pp. 221-229 ◽  
Author(s):  
Zhaojing Meng ◽  
Patrick A. Limbach
Keyword(s):  
Mass Spectrometry ◽  
Electrospray Ionization ◽  
Electrospray Ionization Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Ionization Mass Spectrometry ◽  
Ionization Mass ◽  
Minimal Component ◽  
Rapid Characterization ◽  
Sequential Generation

Nozzle-skimmer dissociation in combination with de novo sequencing was investigated as an approach for increasing the throughput of oligonucleotide analysis attainable by electrospray ionization mass spectrometry. An experimental method allowing for the sequential generation of precursor and fragment ion data during direct infusion of samples was developed. These data can then be used with readily available de novo sequencing software to characterize small oligonucleotides. When this approach was applied to mixtures of oligonucleotides, it was found that de novo sequencing becomes limited due to spectral congestion and overlapping oligonucleotide m/z dissociation product values. Self-packed C18 microspray emitters were investigated as a means of reducing spectral complexity. It was found that such emitters allow for the analysis of oligonucleotide mixtures with minimal component overlap, and these emitters provide additional benefits of pre-concentrating and desalting the sample. These developments can provide a route for the more rapid characterization of ribonucleic acid endonuclease digestion mixtures.

A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry

The Analyst ◽  
2011 ◽  
Vol 136 (1) ◽  
pp. 113-119 ◽  
Author(s):  
Chihiro Nakajima ◽  
Hiroki Kuyama ◽  
Takashi Nakazawa ◽  
Osamu Nishimura ◽  
Susumu Tsunasawa
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing

De novo sequencing and characterization of a novel Bowman–Birk inhibitor from Lathyrus sativus L. seeds by electrospray mass spectrometry

2012 ◽  
Vol 8 (12) ◽  
pp. 3232 ◽  
Author(s):  
Rachele Tamburino ◽  
Valeria Severino ◽  
Annamaria Sandomenico ◽  
Menotti Ruvo ◽  
Augusto Parente ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Electrospray Mass Spectrometry ◽  
De Novo ◽  
De Novo Sequencing ◽  
Lathyrus Sativus ◽  
Lathyrus Sativus L
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