scholarly journals IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins

2013 ◽  
Vol 90 ◽  
pp. 77-84 ◽  
Author(s):  
Florian P. Breitwieser ◽  
Jacques Colinge
Keyword(s):  
Quantitative Analysis ◽  
Software Tool ◽  
Modified Proteins

scholarly journals A quantitative analysis software tool for mass spectrometry–based proteomics

2008 ◽  
Vol 5 (4) ◽  
pp. 319-322 ◽  
Author(s):  
Sung Kyu Park ◽  
John D Venable ◽  
Tao Xu ◽  
John R Yates
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Software Tool ◽  
Analysis Software

scholarly journals pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation

2021 ◽  
Author(s):  
Weiqian Cao ◽  
Siyuan Kong ◽  
Wenfeng Zeng ◽  
Pengyun Gong ◽  
Biyun Jiang ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Large Scale ◽  
Missing Values ◽  
Software Tool ◽  
Software Tools ◽  
Residual Network ◽  
Site Specific ◽  
Carcinoma Cell Lines ◽  
L1 Cell Adhesion Molecule

Interpreting large-scale glycoproteomic data for intact glycopeptide identification has been tremendously advanced by software tools. However, software tools for quantitative analysis of intact glycopeptides remain lagging behind, which greatly hinders exploring the differential expression and functions of site-specific glycosylation in organisms. Here, we report pGlycoQuant, a generic software tool for accurate and convenient quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant enables intact glycopeptide quantitation with very low missing values via a deep residual network, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco. The pGlycoQuant-based site-specific N-glycoproteomic study conducted here quantifies 6435 intact N-glycopeptides in three hepatocellular carcinoma cell lines with different metastatic potentials and, together with in vitro molecular biology experiments, illustrates core fucosylation at site 979 of the L1 cell adhesion molecule (L1CAM) as a potential regulator of HCC metastasis. pGlycoQuant is freely available at https://github.com/expellir-arma/pGlycoQuant/releases/. We have demonstrated pGlycoQuant to be a powerful tool for the quantitative analysis of site-specific glycosylation and the exploration of potential glycosylation-related biomarker candidates, and we expect further applications in glycoproteomic studies.

FDG PET/CT in cancer therapy monitoring

2011 ◽  
Vol 50 (02) ◽  
pp. 83-92 ◽  
Author(s):  
S. Renisch ◽  
R. Opfer ◽  
T. Derlin ◽  
R. Buchert ◽  
I. C. Carlsen ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Cancer Therapy ◽  
Fdg Pet ◽  
Visual Analysis ◽  
Therapy Monitoring ◽  
Software Tool ◽  
Computer Assisted ◽  
Pet Ct ◽  
Fdg Pet Ct ◽  
Assisted Analysis

SummaryObjectives: We developed and tested a software tool for computer-assisted analysis of FDG-PET/CT in cancer therapy monitoring. The tool provides automatic semi-quantitative analysis of a baseline scan together with up to two follow-up scans (standardized uptake values, glycolytic volume). The tool also supports visual analysis by local spatial registration which allows display of tumor lesions with the same orientation in all scans. The tool’s stability and accuracy was tested at typical everyday image quality. Patients, methods: Ten unselected cancer patients in whom three FDG PET/CT scans had been performed were included. A total of 18 lesions were analyzed. Results: Automatic lesion tracking worked properly in all lesions but one. In this lesion local coregistration had to be adjusted manually tuwhich, however, is easily performed with the tool. Semi-automatic lesion segmentation and fully automatic semi-quantitative analysis worked properly in all cases. Computer-assisted analysis was significantly less time consuming than manual analysis. Conclusions: The novel software tool appears useful for analysis of FDGPET/ CT in cancer therapy monitoring in clinical routine patient care.

ANTONIA Perfusion and Stroke

2014 ◽  
Vol 53 (06) ◽  
pp. 469-481 ◽  
Author(s):  
B. Cheng ◽  
A. Kemmling ◽  
G. Thomalla ◽  
J. Fiehler ◽  
N. D. Forkert
Keyword(s):  
Ischemic Stroke ◽  
Quantitative Analysis ◽  
Acute Ischemic Stroke ◽  
Arterial Input Function ◽  
Software Tool ◽  
Input Function ◽  
Lesion Volume ◽  
Acute Ischemic Stroke Patient ◽  
Stroke Research ◽  
Selection Of

SummaryObjectives: The objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of additional datasets for the specific purpose of acute ischemic stroke patient dataset evaluation.Methods: Three different methods for the analysis of DSC or DCE PWI datasets are currently implemented in ANTONIA, which can be case-specifically selected based on the study protocol. These methods comprise a curve fitting method as well as a deconvolution-based and deconvolution-free method integrating a previously defined arterial input function. The perfusion analysis is extended for the purpose of acute ischemic stroke analysis by additional methods that enable an automatic atlas-based selection of the arterial input function, an analysis of the perfusion-diffusion and DWI-FLAIR mismatch as well as segmentation-based volumetric analyses.Results: For reliability evaluation, the de-scribed software tool was used by two ob-servers for quantitative analysis of 15 data-sets from acute ischemic stroke patients to extract the acute lesion core volume, FLAIR ratio, perfusion-diffusion mismatch volume with manually as well as automatically selected arterial input functions, and follow-up lesion volume. The results of this evaluation revealed that the described software tool leads to highly reproducible results for all parameters if the automatic arterial input function selection method is used.Conclusion: Due to the broad selection of processing methods that are available in the software tool, ANTONIA is especially helpful to support image-based perfusion and acute ischemic stroke research projects.

Quantitative analysis of polyethylene glycol (PEG) in PEG-modified proteins/cytokines by aqueous two-phase systems

1994 ◽  
Vol 29 (3-4) ◽  
pp. 237-250 ◽  
Author(s):  
Cristina Delgado ◽  
Farooq Malik ◽  
Barbara Selisko ◽  
Derek Fischer ◽  
Gillian E. Francis
Keyword(s):  
Polyethylene Glycol ◽  
Quantitative Analysis ◽  
Two Phase ◽  
Aqueous Two Phase Systems ◽  
Phase Systems ◽  
Modified Proteins

scholarly journals KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons

Traffic ◽  
2016 ◽  
Vol 18 (1) ◽  
pp. 71-88 ◽  
Author(s):  
Sylvia Neumann ◽  
Romain Chassefeyre ◽  
George E. Campbell ◽  
Sandra E. Encalada
Keyword(s):  
Quantitative Analysis ◽  
Intracellular Transport ◽  
Software Tool

UDAT: Compound quantitative analysis of text using machine learning

2020 ◽  
Author(s):  
Lior Shamir
Keyword(s):  
Pattern Recognition ◽  
Quantitative Analysis ◽  
Open Source ◽  
Software Tool ◽  
Large Set ◽  
Large Databases ◽  
Command Line Tool ◽  
Pattern Recognition Analysis ◽  
Text Content ◽  
Computing Machines

Abstract Computing machines allow quantitative analysis of large databases of text, providing knowledge that is difficult to obtain without using automation. This article describes Universal Data Analysis of Text (UDAT) —a text analysis method that extracts a large set of numerical text content descriptors from text files and performs various pattern recognition tasks such as classification, similarity between classes, correlation between text and numerical values, and query by example. Unlike several previously proposed methods, UDAT is not based on frequency of words and links between certain key words and topics. The method is implemented as an open-source software tool that can provide detailed reports about the quantitative analysis of sets of text files, as well as exporting the numerical text content descriptors in the form of comma-separated values files to allow statistical or pattern recognition analysis with external tools. It also allows the identification of specific text descriptors that differentiate between classes or correlate with numerical values and can be applied to problems related to knowledge discovery in domains such as literature and social media. UDAT is implemented as a command-line tool that runs in Windows, and the open source is available and can be compiled in Linux systems. UDAT can be downloaded from http://people.cs.ksu.edu/∼lshamir/downloads/udat.

Questioned Document Examination Using CEDAR-FOX

2018 ◽  
Vol 28 ◽  
pp. 15-26 ◽  
Author(s):  
Sargur N. Srihari ◽  
Barish Srinivasan ◽  
Kartik Desai
Keyword(s):  
Quantitative Analysis ◽  
Science And Technology ◽  
Software Tool ◽  
Software System ◽  
Document Examination ◽  
Qualitative Measure

Handwriting verification casework often involves comparing the writing in a questioned document with samples of known writing. This paper describes the use of CEDAR-FOX, a software tool for questioned document examination, in a case involving extended writing. The different steps involved from scanning the documents to obtaining a nine-point qualitative measure are described. The various algorithms used, along with a demonstration of its. functionalities on the case are also described. The paper serves two purposes: a guide to using a stateof- the-art software system for a quantitative analysis of handwriting, and an introduction to the science and technology of the software. Purchase Article - $10

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