PTMSearchPlus: Software Tool for Automated Protein Identification and Post-Translational Modification Characterization by Integrating Accurate Intact Protein Mass and Bottom-Up Mass Spectrometric Data Searches

2009 ◽  
Vol 81 (20) ◽  
pp. 8387-8395 ◽  
Author(s):  
Vilmos Kertesz ◽  
Heather M. Connelly ◽  
Brian K. Erickson ◽  
Robert L. Hettich
Keyword(s):  
Protein Identification ◽  
Software Tool ◽  
Mass Spectrometric ◽  
Intact Protein ◽  
Post Translational Modification ◽  
Bottom Up ◽  
Mass Spectrometric Data ◽  
Spectrometric Data ◽  
Protein Mass

Preprocessing of tandem mass spectrometric data to support automatic protein identification

PROTEOMICS ◽  
2003 ◽  
Vol 3 (8) ◽  
pp. 1597-1610 ◽  
Author(s):  
Marc Gentzel ◽  
Thomas Köcher ◽  
Saravanan Ponnusamy ◽  
Matthias Wilm
Keyword(s):  
Protein Identification ◽  
Mass Spectrometric ◽  
Tandem Mass ◽  
Mass Spectrometric Data ◽  
Spectrometric Data ◽  
Tandem Mass Spectrometric

scholarly journals PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes

2016 ◽  
Vol 13 (4) ◽  
pp. 16-23 ◽  
Author(s):  
Canan Has ◽  
Sergey A. Lashin ◽  
Alexey Kochetov ◽  
Jens Allmer
Keyword(s):  
Protein Identification ◽  
Gene Annotation ◽  
Major Gene ◽  
Peptide Identification ◽  
Mass Spectrometric ◽  
Coding Region ◽  
Mass Spectrometric Data ◽  
Spectrometric Data ◽  
A Genome ◽  
Gene Models

Abstract Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered. Mass spectrometry allows the identification and sequencing of proteins as major gene products; and it is only these proteins that conclusively show whether a part of a genome is a coding region or not to result in phenotypes. Therefore, in the field of proteogenomics, the validation of computational methods is done by exploiting mass spectrometric data. As a result, identification of novel protein coding regions, validation of current gene models, and determination of upstream and downstream regions of genes can be achieved. In this paper, we present new functionality for our proteogenomic tool, PGMiner which performs all proteogenomic steps like acquisition of mass spectrometric data, peptide identification against preprocessed sequence databases, assignment of statistical confidence to identified peptides, mapping confident peptides to gene models, and result visualization. The extensions cover determining proteotypic peptides and thus unambiguous protein identification. Furthermore, peptides conflicting with gene models can now automatically assessed within the context of predicted alternative open reading frames.

Anacyclamide D8P, a prenylated cyanobactin from a Sphaerospermopsis sp. cyanobacterium

2017 ◽  
Author(s):  
Joana Martins ◽  
Niina Leikoski ◽  
Matti Wahlsten ◽  
Joana Azevedo ◽  
Jorge Antunes ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Cyclic Peptides ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Tyrosine Residue ◽  
Biosynthetic Gene ◽  
Post Translational Modification ◽  
Biological Assays ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

Cyanobactins are a family of linear and cyclic peptides produced through the post-translational modification of short precursor peptides. Anacyclamides are macrocyclic cyanobactins with a highly diverse sequence that are common in the genus <i>Anabaena</i>. A mass spectrometry-based screening of potential cyanobactin producers led to the discovery of a new prenylated member of this family of compounds, anacyclamide D8P (<b>1</b>), from <i>Sphaerospermopsis</i> sp. LEGE 00249. The anacyclamide biosynthetic gene cluster (<i>acy</i>) encoding the novel macrocyclic prenylated cyanobactin, was sequenced. Heterologous expression of the acy gene cluster in <i>Escherichia</i> <i>coli</i> established the connection between genomic and mass spectrometric data. Unambiguous establishment of the type and site of prenylation required the full structural elucidation of <b>1</b> using Nuclear Magnetic Resonance (NMR), which demonstrated that a forward prenylation occurred on the tyrosine residue. Compound <b>1</b> was tested in pharmacologically or ecologically relevant biological assays and revealed moderate antimicrobial activity towards the fouling bacterium <i>Halomonas aquamarina</i> CECT 5000.<br>

Application of Factor Analysis in Imaging Mass Spectrometric Data Analysis

2014 ◽  
Vol 42 (8) ◽  
pp. 1099-1103 ◽  
Author(s):  
Yi CHEN ◽  
Fei TANG ◽  
Tie-Gang LI ◽  
Jiu-Ming HE ◽  
Zeper ABLIZ ◽  
...  
Keyword(s):  
Factor Analysis ◽  
Data Analysis ◽  
Mass Spectrometric ◽  
Mass Spectrometric Data ◽  
Spectrometric Data
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