InsPecT:  Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra

2005 ◽  
Vol 77 (14) ◽  
pp. 4626-4639 ◽  
Author(s):  
Stephen Tanner ◽  
Hongjun Shu ◽  
Ari Frank ◽  
Ling-Chi Wang ◽  
Ebrahim Zandi ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Modified Peptides

Method to Correlate Tandem Mass Spectra of Modified Peptides to Amino Acid Sequences in the Protein Database

1995 ◽  
Vol 67 (8) ◽  
pp. 1426-1436 ◽  
Author(s):  
John R. Yates ◽  
Jimmy K. Eng ◽  
Ashley L. McCormack ◽  
David. Schieltz
Keyword(s):  
Amino Acid ◽  
Mass Spectra ◽  
Amino Acid Sequences ◽  
Tandem Mass ◽  
Protein Database ◽  
Tandem Mass Spectra ◽  
Modified Peptides

scholarly journals MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

2017 ◽  
Author(s):  
Hosein Mohimani ◽  
Alexey Gurevich ◽  
Kelsey L. Alexander ◽  
C. Benjamin Naman ◽  
Tiago Leão ◽  
...  
Keyword(s):  
Natural Products ◽  
Mass Spectra ◽  
Large Scale ◽  
Software Tool ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Modified Peptides ◽  
New Algorithms ◽  
Large Scale Screening ◽  
Metagenome Mining

AbstractRibosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that include many antibiotics and a variety of other bioactive compounds. While recent breakthroughs in RiPP discovery raised the challenge of developing new algorithms for their analysis, peptidogenomic-based identification of RiPPs by combining genome/metagenome mining with analysis of tandem mass spectra remains an open problem. We present here MetaRiPPquest, a software tool for addressing this challenge that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just six genomic and metagenomic datasets, MetaRiPPquest identified 27 known and discovered 5 novel RiPP natural products.

α-Methylene-β-Lactone Probe for Measuring Live-Cell Reactions of Small Molecules

2020 ◽  
Author(s):  
Lei Wang ◽  
Louis Riel ◽  
Bekim Bajrami ◽  
Bin Deng ◽  
Amy Howell ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Live Cell ◽  
Live Cells ◽  
The Novel ◽  
Proteomics Analysis ◽  
Chemical Proteomics ◽  
Tandem Mass Spectra ◽  
Modified Peptides ◽  
Covalent Probes ◽  
Ht 29

The novel use of the α-methylene-β-lactone (MeLac) moiety as a warhead of multiple electrophilic sites is reported. In this study, we demonstrate that a MeLac-alkyne is a competent covalent probe and reacts with diverse proteins in live cells. Proteomics analysis of affinity-enriched samples identifies probe-reacted proteins, resolves their modified peptides/residues, and thus characterizes probe-protein reactions. Unique methods are developed to evaluate confidence in the identification of the reacted proteins and modified peptides. Tandem mass spectra of the peptides reveal that MeLac reacts with nucleophilic cysteine, serine, lysine, threonine, and tyrosine residues, through either Michael addition or acyl addition. A peptide-centric proteomics platform, using MeLac-alkyne as the measurement probe, successfully analyzes the Orlistat selectivity in live HT-29 cells. MeLac is a versatile warhead demonstrating enormous potential to expedite the development of covalent probes and inhibitors in interrogating protein (re)activity. MeLac-empowered platforms in chemical proteomics are widely adaptable for measuring the live-cell action of reactive molecules.

MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides

2021 ◽  
Author(s):  
Xiaoyu Yang ◽  
Pedatsur Neta ◽  
Yuri A. Mirokhin ◽  
Dmitrii V. Tchekhovskoi ◽  
Concepcion A. Remoroza ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Tandem Mass ◽  
Tandem Mass Spectra
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