scholarly journals Detecting modifications in proteomics experiments with Param-Medic

2018 ◽  
Author(s):  
Damon May ◽  
Kaipo Tamura ◽  
William Noble
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Data Sets ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Accurate Knowledge ◽  
Peptide Database ◽  
Public Data ◽  
Experimental Parameters ◽  
Experimental Metadata

Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inac- curate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling, tandem mass tags, and phosphorylation, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open source Python and C++ implementations in a new version of the software tool Param-Medic.

scholarly journals DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets

2009 ◽  
Vol 9 (3) ◽  
pp. 486-496 ◽  
Author(s):  
Vladislav A. Petyuk ◽  
Anoop M. Mayampurath ◽  
Matthew E. Monroe ◽  
Ashoka D. Polpitiya ◽  
Samuel O. Purvine ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Systematic Errors ◽  
Data Sets ◽  
Tandem Mass ◽  
Mass Measurements ◽  
Tandem Mass Spectra

scholarly journals Protocol for analysis of glycoproteomics LC-MS data using GlycReSoft

2020 ◽  
Author(s):  
Joshua A. Klein ◽  
Joseph Zaia
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Database Search ◽  
Peptide Sequence ◽  
Data Sets ◽  
Tandem Mass ◽  
Exact Mass ◽  
Tandem Mass Spectra ◽  
Search Results ◽  
Data Files

Summary/AbstractThe GlycReSoft software tool allows users to process glycoproteomics LC-MS data sets. The tool accepts proteomics database search results or a user-defined list of proteins in the sample. GlycReSoft processes LC-MS data to yield deconvoluted exact mass values. The user has the option to import a list of theoretical glycans from an external database, a curated glycan list, or a measured glycome. The tool assembles a list of theoretical glycopeptides from the lists of theoretical glycans and proteins, respectively. The program then scores the tandem mass spectra in the LC-MS data files and provides graphical views of the identified glycopeptides for each protein in the sample, and the set of glycoforms identified for each peptide sequence.

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

scholarly journals SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database

2001 ◽  
Vol 17 (Suppl 1) ◽  
pp. S13-S21 ◽  
Author(s):  
V. Bafna ◽  
N. Edwards
Keyword(s):  
Probabilistic Model ◽  
Mass Spectra ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Peptide Database

scholarly journals mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44913 ◽  
Author(s):  
Timo H. J. Niedermeyer ◽  
Martin Strohalm
Keyword(s):  
Mass Spectra ◽  
Cyclic Peptide ◽  
Software Tool ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals mMass as a software tool for the annotation of cyclic peptide tandem mass spectra

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
THJ Niedermeyer ◽  
M Strohalm
Keyword(s):  
Mass Spectra ◽  
Cyclic Peptide ◽  
Software Tool ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

2008 ◽  
Vol 24 (7) ◽  
pp. 1021-1023 ◽  
Author(s):  
A. M. Mayampurath ◽  
N. Jaitly ◽  
S. O. Purvine ◽  
M. E. Monroe ◽  
K. J. Auberry ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Tandem Mass ◽  
Mass Determination ◽  
Monoisotopic Mass ◽  
Tandem Mass Spectra

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.

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