Spectral quality overrides software score―A brief tutorial on the analysis of peptide fragmentation data for mass spectrometry laymen

2021 ◽  
Vol 56 (2) ◽  
Author(s):  
Simone König
Keyword(s):  
Mass Spectrometry ◽  
Peptide Fragmentation ◽  
Spectral Quality

scholarly journals Characterization of a novel + 70 Da modification in rhGM-CSF expressed in E. coli using chemical assays in combination with mass spectrometry

Amino Acids ◽  
2021 ◽  
Author(s):  
Magdalena Widgren Sandberg ◽  
Jakob Bunkenborg ◽  
Stine Thyssen ◽  
Martin Villadsen ◽  
Thomas Kofoed
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Peptide Mapping ◽  
Covalent Modification ◽  
Peptide Fragmentation ◽  
Tandem Mass ◽  
E Coli ◽  
Gm Csf ◽  
Fragmentation Behavior ◽  
Macrophage Colony

AbstractGranulocyte-macrophage colony-stimulating factor (GM-CSF) is a cytokine and a white blood cell growth factor that has found usage as a therapeutic protein. During analysis of different fermentation batches of GM-CSF recombinantly expressed in E. coli, a covalent modification was identified on the protein by intact mass spectrometry. The modification gave a mass shift of + 70 Da and peptide mapping analysis demonstrated that it located to the protein N-terminus and lysine side chains. The chemical composition of C4H6O was found to be the best candidate by peptide fragmentation using tandem mass spectrometry. The modification likely contains a carbonyl group, since the mass of the modification increased by 2 Da by reduction with borane pyridine complex and it reacted with 2,4-dinitrophenylhydrazine. On the basis of chemical and tandem mass spectrometry fragmentation behavior, the modification could be attributed to crotonaldehyde, a reactive compound formed during lipid peroxidation. A low recorded oxygen pressure in the reactor during protein expression could be linked to the formation of this compound. This study shows the importance of maintaining full control over all reaction parameters during recombinant protein production.

Data Mining in Protein Identification by Tandem Mass Spectrometry

2011 ◽  
pp. 472-478
Author(s):  
Haipeng Wang
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Tandem Mass Spectrometry ◽  
Large Scale ◽  
Protein Identification ◽  
Peptide Fragmentation ◽  
Tandem Mass ◽  
Fragmentation Pattern ◽  
Post Translational Modification ◽  
Challenges And Opportunities

Protein identification (sequencing) by tandem mass spectrometry is a fundamental technique for proteomics which studies structures and functions of proteins in large scale and acts as a complement to genomics. Analysis and interpretation of vast amounts of spectral data generated in proteomics experiments present unprecedented challenges and opportunities for data mining in areas such as data preprocessing, peptide-spectrum matching, results validation, peptide fragmentation pattern discovery and modeling, and post-translational modification (PTM) analysis. This article introduces the basic concepts and terms of protein identification and briefly reviews the state-of-the-art relevant data mining applications. It also outlines challenges and future potential hot spots in this field.

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.

Mining a Tandem Mass Spectrometry Database To Determine the Trends and Global Factors Influencing Peptide Fragmentation

2003 ◽  
Vol 75 (22) ◽  
pp. 6251-6264 ◽  
Author(s):  
Eugene A. Kapp ◽  
Frédéric Schütz ◽  
Gavin E. Reid ◽  
James S. Eddes ◽  
Robert L. Moritz ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Peptide Fragmentation ◽  
Tandem Mass ◽  
Factors Influencing

Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry

2017 ◽  
Vol 28 (6) ◽  
pp. 1216-1226 ◽  
Author(s):  
Bhanuramanand Kuchibhotla ◽  
Sankara Rao Kola ◽  
Jagannadham V. Medicherla ◽  
Swamy V. Cherukuvada ◽  
Vishnu M. Dhople ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Peptide Fragmentation ◽  
Labeling Method
Sign in / Sign up

Export Citation Format

Share Document