scholarly journals Finding and using diagnostic ions in collision induced crosslinked peptide fragmentation spectra

2019 ◽  
Vol 444 ◽  
pp. 116184 ◽  
Author(s):  
Barbara Steigenberger ◽  
Herbert B. Schiller ◽  
Roland J. Pieters ◽  
Richard A. Scheltema
Keyword(s):  
Peptide Fragmentation ◽  
Diagnostic Ions

scholarly journals Small Mass but Strong Information: Diagnostic Ions Provide Crucial Clues to Correctly Identify Histone Lysine Modifications

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 18
Author(s):  
Alaa Hseiky ◽  
Marion Crespo ◽  
Sylvie Kieffer-Jaquinod ◽  
François Fenaille ◽  
Delphine Pflieger
Keyword(s):  
Amino Acid ◽  
Small Mass ◽  
Mass Region ◽  
Amino Acid Sequences ◽  
Lysine Modification ◽  
Lysine Residues ◽  
Two Factors ◽  
Low Mass ◽  
Diagnostic Ions

(1) Background: The proteomic analysis of histones constitutes a delicate task due to the combination of two factors: slight variations in the amino acid sequences of variants and the multiplicity of post-translational modifications (PTMs), particularly those occurring on lysine residues. (2) Methods: To dissect the relationship between both aspects, we carefully evaluated PTM identification on lysine 27 from histone H3 (H3K27) and the artefactual chemical modifications that may lead to erroneous PTM determination. H3K27 is a particularly interesting example because it can bear a range of PTMs and it sits nearby residues 29 and 31 that vary between H3 sequence variants. We discuss how the retention times, neutral losses and immonium/diagnostic ions observed in the MS/MS spectra of peptides bearing modified lysines detectable in the low-mass region might help validate the identification of modified sequences. (3) Results: Diagnostic ions carry key information, thereby avoiding potential mis-identifications due to either isobaric PTM combinations or isobaric amino acid-PTM combinations. This also includes cases where chemical formylation or acetylation of peptide N-termini artefactually occurs during sample processing or simply in the timeframe of LC-MS/MS analysis. Finally, in the very subtle case of positional isomers possibly corresponding to a given mass of lysine modification, the immonium and diagnostic ions may allow the identification of the in vivo structure.

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.

Search for Melanoma Markers in Plasma and Serum Samples

2005 ◽  
Vol 11 (3) ◽  
pp. 353-360 ◽  
Author(s):  
Roberta Seraglia ◽  
Susanna Vogliardi ◽  
Graziella Allegri ◽  
Stefano Comai ◽  
Mario Lise ◽  
...  
Keyword(s):  
High Frequency ◽  
Healthy Subjects ◽  
Ionic Species ◽  
Low Molecular Weight ◽  
Ionization Mass ◽  
Plasma Samples ◽  
Serum Samples ◽  
Blood Samples ◽  
Melanoma Patients ◽  
Diagnostic Ions

Fourteen blood samples from patients with melanomas and 11 blood samples from healthy subjects were analyzed by matrix-assisted laser desorption/ionization mass spectrometry. The study focussed on species of low molecular weight, in the 800–5000 Da range, present in plasma and sera. While for healthy subjects plasma samples lead to the production of a higher number of ionic species, for melanoma patients a high number of diagnostic ions, present with high frequency and with quite high relative abundance, are present, in particular, in serum samples and, to a lesser extent, also in plasma. Since plasma samples are obtained more easily in comparison to sera, it is possible to suggest that plasma can also be used for these studies.

scholarly journals On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

2011 ◽  
Vol 83 (3) ◽  
pp. 790-796 ◽  
Author(s):  
Sujun Li ◽  
Randy J. Arnold ◽  
Haixu Tang ◽  
Predrag Radivojac
Keyword(s):  
Peptide Fragmentation ◽  
Spectrum Prediction ◽  
Fragmentation Spectrum

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.

Analytical Strategy for the Regulatory Control of Residues of Chloramphenicol in Meat: Preliminary Studies in Milk

1992 ◽  
Vol 75 (2) ◽  
pp. 245-256 ◽  
Author(s):  
H J Keukens ◽  
M M L Aerts ◽  
W A Traag ◽  
J F M Nouws ◽  
W G De Ruig ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Collaborative Study ◽  
Regulatory Control ◽  
Veterinary Drug ◽  
Uv Spectrum ◽  
Analytical Strategy ◽  
Column Liquid Chromatographic ◽  
Set Up ◽  
Diagnostic Ions ◽  
Liquid Chromatographic

Abstract An analytical strategy Is described for the regulatory control of residues of the veterinary drug chloramphenicol (CAP) In meat. Screening is performed directly in meat by a simple immunochemical card test with a limit of detection of about 2 μg/kg. Statistical evaluation of a collaborative study involving 13 laboratories showed that at CAP concentrations exceeding 8 μg/kg, no false negatives are found (N = 554). In positive samples, CAP Is quantltated with a routinely applicable, collaboratively tested column liquid chromatographic method with a limit of detection of about 1 μg/kg. At concentrations exceeding 10 μg/kg, the Identity of CAP Is established by Its UV spectrum obtained by using diode-array UV/VIS detection. A further confirmation can be obtained by the combination of gas chromatography/ mass selective detection In the electron Impact mode. Using 2 diagnostic Ions (m/z 225 and 208), the limit of identification Is about 5 μg/kg. The combination of the different analytical principles ensures reliable quantitation and Identification of CAP in positive samples, as established experimentally in Incurred samples and spiked samples (n > 100), and theoretically by the estimation of the uncertainty factor. The proposed set-up makes a regulatory program possible in which screening can be performed In a simple laboratory environment, followed by quantitation and Identification under more sophisticated conditions. Preliminary experiments Indicate that the analytical strategy Is also applicable to the control of CAP in milk. Application of mass spectrometry with negative chemical ionization permits the confirmation of CAP concentrations as low as 0.2 μg/L.

Gas-Phase Peptide Fragmentation Induced by Hydrogen Attachment, from Principle to Sequencing of Amide Nitrogen-Methylated Peptides

2020 ◽  
Vol 92 (24) ◽  
pp. 15773-15780
Author(s):  
Daiki Asakawa ◽  
Hidenori Takahashi ◽  
Shinichi Iwamoto ◽  
Koichi Tanaka
Keyword(s):  
Gas Phase ◽  
Peptide Fragmentation ◽  
Amide Nitrogen
Sign in / Sign up

Export Citation Format

Share Document