Browsing Department of Biomedicine by Journals "Journal of Proteome Research"
Now showing items 1-7 of 7
-
Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets
(Peer reviewed; Journal article, 2018)Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected ... -
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra
(Peer reviewed; Journal article, 2014)De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, ... -
In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis: presenting a comprehensive picture of pathways and processes affected by multiple sclerosis
(Peer reviewed; Journal article, 2017)In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry ... -
PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data
(Journal article; Peer reviewed, 2021)Mass spectrometry-based proteomics is a high-throughput technology generating ever-larger amounts of data per project. However, storing, processing, and interpreting these data can be a challenge. A key element in simplifying ... -
Proteomics Standards Initiative Extended FASTA Format
(Peer reviewed; Journal article, 2019)Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most ... -
SearchGUI: a highly adaptable common interface for proteomics search and de novo engines
(Peer reviewed; Journal article, 2018)Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide ... -
thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files
(Peer reviewed; Journal article, 2011)The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has ...