Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry

2005 ◽  
pp. 326-341 ◽  
Author(s):  
Ari Frank ◽  
Stephen Tanner ◽  
Pavel Pevzner
Keyword(s):  
Mass Spectrometry ◽  
Database Search ◽  
Peptide Sequence

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>

Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry

2005 ◽  
Vol 4 (4) ◽  
pp. 1287-1295 ◽  
Author(s):  
Ari Frank ◽  
Stephen Tanner ◽  
Vineet Bafna ◽  
Pavel Pevzner
Keyword(s):  
Mass Spectrometry ◽  
Database Search ◽  
Peptide Sequence

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 Mass Spectrometric Analysis of Multiple Pertussis Toxins and Toxoids

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Yulanda M. Williamson ◽  
Hercules Moura ◽  
David Schieltz ◽  
Jon Rees ◽  
Adrian R. Woolfitt ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Immune Response ◽  
Mass Spectrometric ◽  
Peptide Sequence ◽  
Spectrometric Analysis ◽  
Vaccine Preventable Disease ◽  
Label Free ◽  
Chemically Modified ◽  
Quantification Method ◽  
Major Virulence Factor

Bordetella pertussis(Bp) is the causative agent of pertussis, a vaccine preventable disease occurring primarily in children. In recent years, there has been increased reporting of pertussis. Current pertussis vaccines are acellular and consist of Bp proteins including the major virulence factor pertussis toxin (Ptx), a 5-subunit exotoxin. Variation in Ptx subunit amino acid (AA) sequence could possibly affect the immune response. A blind comparative mass spectrometric (MS) analysis of commercially available Ptx as well as the chemically modified toxoid (Ptxd) from licensed vaccines was performed to assess peptide sequence and AA coverage variability as well as relative amounts of Ptx subunits. Qualitatively, there are similarities among the various sources based on AA percent coverages and MS/MS fragmentation profiles. Additionally, based on a label-free mass spectrometry-based quantification method there is differential relative abundance of the subunits among the sources.

scholarly journals Development of an MS Workflow Based on Combining Database Search Engines for Accurate Protein Identification and Its Validation to Identify the Serum Proteomic Profile in Female Stress Urinary Incontinence

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Sara El Jadid ◽  
Taoufik Bensellak ◽  
Raja Touahni ◽  
Ahmed Moussa
Keyword(s):  
Mass Spectrometry ◽  
Urinary Incontinence ◽  
Stress Urinary Incontinence ◽  
Search Engines ◽  
High Performance ◽  
Protein Identification ◽  
Computing Time ◽  
Database Search ◽  
Female Stress Urinary Incontinence ◽  
Accurate Analysis

A critical stage of shotgun proteomics is database search, a process which attempts to match the experimental spectra to the theoretical one. Given the considerable time and effort spent in analysis, it is self-evident for a researcher to aspire for rigorous computational analysis and a more confident and accurate peptide/protein identification. Mass spectrometry (MS) has been applied across several clinical disciplines. The pathophysiology of Stress Urinary Incontinence (SUI), caused by a damaged pelvic floor, has become a boundless disease altering the quality of life worldwide. Although some studies pointed markers that can be bioindicators for SUI, these findings raise the issue of sensitivity and specificity. Therefore, it is critical to have a sensitive and specific analytical approach to identify markers that have been associated with protective and deleterious associations in disease. Here, we describe our designed and developed workflow for protein identification from tandem mass spectrometry that uses multiple search engines. We apply our workflow to an existing study addressing the pathophysiology of SUI. We demonstrate how using the combined approach together with high-performance computing techniques can surmount the challenges of complex analyses and extended computing time. We also compare the relative performance of each combination. Our results suggest that a combination of MS-GF+ and COMET represents the best sensitivity-specificity trade-off, outperforming all other tested combinations. The approach was also sensitive and accurately identified a set of protein that was shown to be markers for categories of diseases associated with the pathophysiology of SUI. This workflow was developed to encourage proteomic researchers to adopt MS-based techniques for accurate analysis and to promote MS as a routine tool to the clinical cohorts.

scholarly journals A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Pan Fang ◽  
Yanlong Ji ◽  
Ivan Silbern ◽  
Carmen Doebele ◽  
Momchil Ninov ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Sample Preparation ◽  
Large Scale ◽  
Handling Time ◽  
Database Search ◽  
High Confidence ◽  
Site Specific ◽  
Sample Handling ◽  
Data Processing Tool

Abstract Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that enables confident identification and quantification of intact glycopeptides in complex biological samples. PAC significantly reduces sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search, which increases the identification rates of glycopeptides by 22% compared with conventional strategies. We apply SugarQuant to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determine site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.

Mass spectrometry and database search in the analysis of proteins from the fungusPleurotus ostreatus

PROTEOMICS ◽  
2005 ◽  
Vol 5 (1) ◽  
pp. 67-75 ◽  
Author(s):  
Maja Matis ◽  
Marija ?akelj-Mavri? ◽  
Jasna Peter-Katalini?
Keyword(s):  
Mass Spectrometry ◽  
Database Search
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