De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data

2016 ◽  
pp. 119-134 ◽  
Author(s):  
Mohammad Tawhidul Islam ◽  
Abidali Mohamedali ◽  
Criselda Santan Fernandes ◽  
Mark S. Baker ◽  
Shoba Ranganathan
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Peptide Sequencing ◽  
Mass Spectrometry Data ◽  
Deep Mining ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide ◽  
Resolution Mass

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.

Signal Detection in High-Resolution Mass Spectrometry Data

2008 ◽  
Vol 7 (1) ◽  
pp. 276-285 ◽  
Author(s):  
Dale F. McLerran ◽  
Ziding Feng ◽  
O. John Semmes ◽  
Lisa Cazares ◽  
Timothy W. Randolph
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Signal Detection ◽  
High Resolution Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
High Resolution Mass ◽  
Resolution Mass

scholarly journals De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry

2007 ◽  
Vol 6 (1) ◽  
pp. 114-123 ◽  
Author(s):  
Ari M. Frank ◽  
Mikhail M. Savitski ◽  
Michael L. Nielsen ◽  
Roman A. Zubarev ◽  
Pavel A. Pevzner
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Peptide Sequencing ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

scholarly journals A Simple and Direct Assay for Monitoring Fatty Acid Synthase Activity and Product-Specificity by High-Resolution Mass Spectrometry

Biomolecules ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 118 ◽  
Author(s):  
Magdalena Topolska ◽  
Fernando Martínez-Montañés ◽  
Christer S. Ejsing
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acid ◽  
High Resolution ◽  
Fatty Acid Synthase ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Enzymatic Process ◽  
Product Specificity ◽  
High Resolution Mass ◽  
Resolution Mass

De novo fatty acid synthesis is a pivotal enzymatic process in all eukaryotic organisms. It is involved in the conversion of glucose and other nutrients to fatty acyl (FA) chains, that cells use as building blocks for membranes, energy storage, and signaling molecules. Central to this multistep enzymatic process is the cytosolic type I fatty acid synthase complex (FASN) which in mammals produces, according to biochemical textbooks, primarily non-esterified palmitic acid (NEFA 16:0). The activity of FASN is commonly measured using a spectrophotometry-based assay that monitors the consumption of the reactant NADPH. This assay is indirect, can be biased by interfering processes that use NADPH, and cannot report the NEFA chain-length produced by FASN. To circumvent these analytical caveats, we developed a simple mass spectrometry-based assay that affords monitoring of FASN activity and its product-specificity. In this assay (i) purified FASN is incubated with 13C-labeled malonyl-CoA, acetyl-CoA, and NADPH, (ii) at defined time points the reaction mixture is spiked with an internal NEFA standard and extracted, and (iii) the extract is analyzed directly, without vacuum evaporation and chemical derivatization, by direct-infusion high-resolution mass spectrometry in negative ion mode. This assay supports essentially noise-free detection and absolute quantification of de novo synthetized 13C-labled NEFAs. We demonstrate the efficacy of our assay by determining the specific activity of purified cow FASN and show that in addition to the canonical NEFA 16:0 this enzyme also produces NEFA 12:0, 14:0, 18:0, and 20:0. We note that our assay is generic and can be carried out using commonly available high-resolution mass spectrometers with a resolving power as low as 95,000. We deem that our simple assay could be used as high-throughput screening technology for developing potent FASN inhibitors and for enzyme engineering aimed at modulating the activity and the product-landscape of fatty acid synthases.

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