scholarly journals Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3728
Author(s):  
Taran Driver ◽  
Nikhil Bachhawat ◽  
Leszek J. Frasinski ◽  
Jonathan P. Marangos ◽  
Vitali Averbukh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Peptide Sequence ◽  
Two Dimensional ◽  
Peptide Ions ◽  
Finite Mass ◽  
Protein Database ◽  
Spectra Analysis ◽  
Fragment Ions ◽  
Single Precursor ◽  
The Common

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

scholarly journals Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry

2021 ◽  
Author(s):  
Taran Driver ◽  
Ruediger Pipkorn ◽  
Leszek Frasinski ◽  
Jon P. Marangos ◽  
Marina Edelson-Averbukh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Search Engine ◽  
Database Search ◽  
Peptide Sequence ◽  
Two Dimensional ◽  
Protein Database ◽  
Intact Proteins ◽  
Individual Fragment ◽  
Decomposition Processes ◽  
Complementary Fragment

<div>We present a protein database search engine for the automatic identi?cation of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Since 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the ?first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural speci?city a?orded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides the 2D-PC-MS correlation matching procedure is based on complementary and internal ion correlations, the identi?cation of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.</div>

scholarly journals Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry

2021 ◽  
Author(s):  
Taran Driver ◽  
Ruediger Pipkorn ◽  
Leszek Frasinski ◽  
Jon P. Marangos ◽  
Marina Edelson-Averbukh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Search Engine ◽  
Database Search ◽  
Peptide Sequence ◽  
Two Dimensional ◽  
Protein Database ◽  
Intact Proteins ◽  
Individual Fragment ◽  
Decomposition Processes ◽  
Complementary Fragment

<div>We present a protein database search engine for the automatic identi?cation of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Since 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the ?first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural speci?city a?orded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides the 2D-PC-MS correlation matching procedure is based on complementary and internal ion correlations, the identi?cation of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.</div>

Abstract 613: A Mass Spectrometric Analysis Of Embryonic Zebrafish Proteins

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Margaret B Lucitt ◽  
Tom S Price ◽  
Angel Pizarro ◽  
Weichen Wu ◽  
Anastasia Yocum Yocum ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Mass Spectrometric ◽  
Peptide Sequence ◽  
Spectrometric Analysis ◽  
Cardiovascular Development ◽  
Two Dimensional

Zebrafish is an attractive vertebrate model organism for studies into the molecular mechanisms of cardiovascular development, pathology and pharmacology. Studies into the genetics of protein expression are largely constrained by the availability of specific antibodies. Mass spectrometry based proteomics methods have the potential to overcome these hurdles. This requires firstly an accurate characterization of proteins accessible to targeted quantitative analysis. We applied mass spectrometric proteomic methodology and statistical analysis to create profiles of proteins expressed during zebrafish embryonic development. We detected 1307 proteins from 327,906 peptide sequence identifications at 72 hpf and 120 hpf with false identification rates of less than 1% using two dimensional chromatography tandem mass spectrometry. Close to two thirds of all detected proteins were derived from hypothetical or predicted gene models or were entirely unannotated. Comparison of protein expression in embryos by two dimensional gel electrophoresis differential in gel analysis (DIGE) revealed that proteins involved in energy production and transcription/ translation were relatively more abundant at 72 hpf consistent with the faster synthesis of cellular proteins during organismal growth. Pathway analysis revealed similar expression of proteins at both stages that relate to calcium, insulin receptor, ERK/MAP kinase, vascular epithelial growth factor signaling, and WNT/b-Catenin. Similarly both stages expressed proteins of the complement and coagulation cascades, GM-CSF, PTEN, and sonic hedgehog signaling and inflammatory signals. The data are accessible in a fully searchable database (http://bioinf.itmat.upenn.edu/zebrafish) that links protein identifications to existing resources including the Zebrafish Model Organism Database. This new resource should facilitate the selection of candidate proteins for targeted quantitation and may refine systematic genetic network analysis in vertebrate development and biology. This is the first large-scale proteome analysis of embryonic zebrafish tissue to reveal previously uncharacterized proteins and detect regulated proteins with relevance for cardiovascular function and development.

scholarly journals Uncoiling collagen: a multidimensional mass spectrometry study

The Analyst ◽  
2016 ◽  
Vol 141 (1) ◽  
pp. 157-165 ◽  
Author(s):  
H. J. Simon ◽  
M. A. van Agthoven ◽  
P. Y. Lam ◽  
F. Floris ◽  
L. Chiron ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complex ◽  
Structural Information ◽  
Two Dimensional ◽  
Peptide Ions ◽  
Large Protein ◽  
Tryptic Digest ◽  
Large Protein Complex ◽  
Mass Spectrometry Study ◽  
Multidimensional Mass Spectrometry

Two dimensional mass spectrometry can provide structural information on all peptide ions simultaneously from the tryptic digest of a large protein complex.

scholarly journals High Throughput Analysis of Tandem Mass Spectrometry Data for Peptides

1997 ◽  
Vol 2 (2) ◽  
pp. 28-31
Author(s):  
John R. Yates ◽  
Edwin Carmack ◽  
Lara Hays ◽  
Jimmy Eng
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data ◽  
Mass Analyzer ◽  
Tandem Mass ◽  
Peptide Ions ◽  
High Throughput Analysis ◽  
Substantial Impact ◽  
Fragment Ions

In recent years tandem mass spectrometry has made a substantial impact on the sequence analysis of peptides ( 1 ). In this process peptide ions are dissociated in a collision cell to produce a collection of fragment ions. The m/z values of the fragment ions are determined in the second mass analyzer. Fortuitously, peptide ions fragment primarily around the amide linkages or peptide bonds in a manner that produces a ladder of sequence ions. This method of analysis for peptides has several advantages; high throughput and sensitivity, the ability to analyze peptides contained in mixtures, and lastly the ability to observe covalent modifications to the structure.

AN AUTOMATA APPROACH TO MATCH GAPPED SEQUENCE TAGS AGAINST PROTEIN DATABASE

2005 ◽  
Vol 16 (03) ◽  
pp. 487-497
Author(s):  
YONGHUA HAN ◽  
BIN MA ◽  
KAIZHONG ZHANG
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
De Novo ◽  
De Novo Sequencing ◽  
Computational Method ◽  
Peptide Sequence ◽  
Tandem Mass ◽  
Protein Database ◽  
Matching Algorithm ◽  
Mass Gap

In Biochemistry, tandem mass spectrometry (MS/MS) is the most common method for peptide and protein identifications. One computational method to get a peptide sequence from the MS/MS data is called de novo sequencing, which is becoming more and more important in this area. However De novo sequencing usually can only confidently determine partial sequences, while the undetermined parts are represented by "mass gaps". We call such a partially determined sequence a gapped sequence tag. When a gapped sequence tag is searched in a database for protein identification, the determined parts should match the database sequence exactly, while each mass gap should match a substring of amino acids whose masses add up to the value of the mass gap. In such a case, the standard string matching algorithm does not work any more. In this paper, we present a new efficient algorithm to find the matches of gapped sequence tags in a protein database.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

TRIGLYCERIDE COMPOSITION OF SIXTEEN STRAINS OF MARINE DIATOM

2013 ◽  
Vol 5 (1) ◽  
Author(s):  
Lily M.G. Panggabean ◽  
Abdullah Rasyid ◽  
Zarrah Duniani ◽  
Yana Meliana ◽  
Indah Kurniasih
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acid ◽  
Double Bond ◽  
Unsaturated Fatty Acid ◽  
Ion Trap ◽  
Carbon Chain ◽  
Highly Unsaturated Fatty Acid ◽  
Marine Diatom ◽  
Ion Trap Mass Spectrometry ◽  
Spectra Analysis

Trigliceride or triacylglicerol (TAG) composition in crude oil of sixteen strain of marine diatom has been detected by spectra analyses on an Electrospray - Ion Trap – Mass Spectrometry (ESI-IT-MS) HCT Bruker-Daltonic GmbH instrument with AgNO3 used as coordination ionization agent. Biomass samples of each microalga strain were taken from early and late stationary cultures in f/2 enriched seawater and algal oils were extracted according to Bligh and Dyer. Results from spectra analysis showed that P-Pt-P (C16:0-C16:1-C16:0) were distinguished in TAG from diatom strains Chaetoceros sp.1, Chaetoceros sp.2, Thalasiossira sp.1, Thalasiossira sp.2, Thalasiossira sp.3, Navicula sp. 1, Navicula sp. 2, Navicula sp. 3, Navicula sp. 4, Nitzschia sp. 2 and Amphora sp. In contrast, TAGs in Melosira sp. included P-P-P (C16:0-C16:0-C16:0) and P-P-O (C16:0-C16:0-C18:1) were identified. TAGs from Chaetoceros sp. were the most varies among samples, i.e. P-Pt-P (C16:0-C16:1-C16:0), A-P-M (C20:4-C16:0-C14:0), P-Pt-Lt (C16:0-C16:1-C18:3), P-Pt-A (C16:0-C16:1-C20:4), D-P-P (C22:6-C16:0-C16:0), A-Ln-P (C20:4-C18:2-C16:0). Various TAGs were also detected in Nitzschia sp.2, i.e. P-Pt-M (C16:0-C16:1-C14:0), P-Pt-P (C16:0-C16:1-C16:0), P-Pt-S (C16:0-C16:1-C18:0), P-Pt-A (C16:0-C16:1-C20:4). TAGs composition in Skeletonema strains that similar to those in Nitzschia sp.1 has longer carbon, i.e. P-P-O (C16:0-C16:0-C18:1), P-O-O (C16:0-C18:1-C18:1) and O-O-O (C18:1-C18:1-C18:1). TAGs with longer carbon chain and more double bond including highly unsaturated fatty acid C20:4 were increased with culture age in diatoms Chaetoceros sp.1, Chaetoceros sp.2, Thalasiossira sp.2, Navicula sp.1 and Nitzschia sp. 2.Keywords: diatom, TAG, ESI-IT-MS, f/2, early and late stationary

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