Phosphomatics: interactive interrogation of substrate–kinase networks in global phosphoproteomics datasets

2020 ◽  
Author(s):  
Michael G Leeming ◽  
Sean O’Callaghan ◽  
Luana Licata ◽  
Marta Iannuccelli ◽  
Prisca Lo Surdo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Supplementary Information ◽  
The Internet ◽  
Phosphorylation Sites ◽  
Supplementary Data ◽  
Single Experiment ◽  
Web Resource ◽  
Phosphorylated Peptides

Abstract Motivation Mass spectrometry-based phosphoproteomics can routinely identify and quantify thousands of phosphorylated peptides from a single experiment. However interrogating possible upstream kinases and identifying key literature for phosphorylation sites is laborious and time-consuming. Results Here, we present Phosphomatics—a publicly available web resource for interrogating phosphoproteomics data. Phosphomatics allows researchers to upload phosphoproteomics data and interrogate possible relationships from a substrate-, kinase- or pathway-centric viewpoint. Availability and implementation Phosphomatics is freely available via the internet at: https://phosphomatics.com. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra

2019 ◽  
Author(s):  
Kai Cheng ◽  
Gabrielle Pawlowski ◽  
Xinheng Yu ◽  
Yusen Zhou ◽  
Sriram Neelamegham
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Mass Spectra ◽  
Supplementary Information ◽  
Supplementary Data ◽  
International Union ◽  
Open Source Program ◽  
Source Program ◽  
Wide Range ◽  
Peptide Modifications

Abstract Summary This manuscript describes an open-source program, DrawGlycan-SNFG (version 2), that accepts IUPAC (International Union of Pure and Applied Chemist)-condensed inputs to render Symbol Nomenclature For Glycans (SNFG) drawings. A wide range of local and global options enable display of various glycan/peptide modifications including bond breakages, adducts, repeat structures, ambiguous identifications etc. These facilities make DrawGlycan-SNFG ideal for integration into various glycoinformatics software, including glycomics and glycoproteomics mass spectrometry (MS) applications. As a demonstration of such usage, we incorporated DrawGlycan-SNFG into gpAnnotate, a standalone application to score and annotate individual MS/MS glycopeptide spectrum in different fragmentation modes. Availability and implementation DrawGlycan-SNFG and gpAnnotate are platform independent. While originally coded using MATLAB, compiled packages are also provided to enable DrawGlycan-SNFG implementation in Python and Java. All programs are available from https://virtualglycome.org/drawglycan; https://virtualglycome.org/gpAnnotate. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MetumpX—a metabolomics support package for untargeted mass spectrometry

2019 ◽  
Vol 36 (5) ◽  
pp. 1647-1648 ◽  
Author(s):  
Bilal Wajid ◽  
Hasan Iqbal ◽  
Momina Jamil ◽  
Hafsa Rafique ◽  
Faria Anwar
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Small Molecules ◽  
Software Package ◽  
Life Sciences ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Software Packages ◽  
Develop Software ◽  
User Friendly

Abstract Motivation Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and scripting of software that are mostly not user friendly and lack basic GUIs. As the researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines truly speeding up the learning curve to build software workstations. Therefore, this paper aims to provide MetumpX, a software package that eases in the installation of 103 software by automatically resolving their individual dependencies and also allowing the users to choose which software works best for them. Results MetumpX is a Ubuntu-based software package that facilitate easy download and installation of 103 tools spread across the standard metabolomics pipeline. As far as the authors know MetumpX is the only solution of its kind where the focus lies on automating development of software workstations. Availability and implementation https://github.com/hasaniqbal777/MetumpX-bin. Supplementary information Supplementary data are available at Bioinformatics online.

MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery

2019 ◽  
Vol 35 (16) ◽  
pp. 2870-2872 ◽  
Author(s):  
Xiaotao Shen ◽  
Zheng-Jiang Zhu
Keyword(s):  
Mass Spectrometry ◽  
Data Cleaning ◽  
High Dimensionality ◽  
Supplementary Information ◽  
Data Normalization ◽  
Confounding Factors ◽  
Supplementary Data ◽  
Post Processing ◽  
Metabolomics Data ◽  
Zero Values

Abstract Summary Mass spectrometry-based metabolomics aims to profile the metabolic changes in biological systems and identify differential metabolites related to physiological phenotypes and aberrant activities. However, many confounding factors during data acquisition complicate metabolomics data, which is characterized by high dimensionality, uncertain degrees of missing and zero values, nonlinearity, unwanted variations and non-normality. Therefore, prior to differential metabolite discovery analysis, various types of data cleaning such as batch alignment, missing value imputation, data normalization and scaling are essentially required for data post-processing. Here, we developed an interactive web server, namely, MetFlow, to provide an integrated and comprehensive workflow for metabolomics data cleaning and differential metabolite discovery. Availability and implementation The MetFlow is freely available on http://metflow.zhulab.cn/. Supplementary information Supplementary data are available at Bioinformatics online.

crisscrosslinkeR: identification and visualization of protein–RNA and protein–protein interactions from crosslinking mass spectrometry

2020 ◽  
Author(s):  
Emma H Gail ◽  
Anup D Shah ◽  
Ralf B Schittenhelm ◽  
Chen Davidovich
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
R Package ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Protein Protein Interactions ◽  
Ribonucleoprotein Complexes ◽  
Software Packages ◽  
Different Types ◽  
Publication Quality

Abstract Summary Unbiased detection of protein–protein and protein–RNA interactions within ribonucleoprotein complexes are enabled through crosslinking followed by mass spectrometry. Yet, different methods detect different types of molecular interactions and therefore require the usage of different software packages with limited compatibility. We present crisscrosslinkeR, an R package that maps both protein–protein and protein–RNA interactions detected by different types of approaches for crosslinking with mass spectrometry. crisscrosslinkeR produces output files that are compatible with visualization using popular software packages for the generation of publication-quality figures. Availability and implementation crisscrosslinkeR is a free and open-source package, available through GitHub: github.com/egmg726/crisscrosslinker. Supplementary information Supplementary data are available at Bioinformatics online.

Phosphoproteome Analysis

2005 ◽  
Vol 25 (1-2) ◽  
pp. 33-44 ◽  
Author(s):  
Roberto Raggiaschi ◽  
Stefano Gotta ◽  
Georg C. Terstappen
Keyword(s):  
Mass Spectrometry ◽  
Affinity Chromatography ◽  
Protein Phosphorylation ◽  
Phosphorylation Sites ◽  
Specific Antibodies ◽  
Phosphorylated Proteins ◽  
Cellular Events ◽  
Phosphorylated Peptides ◽  
A Cell ◽  
Experimental Strategies

Protein phosphorylation is directly or indirectly involved in all important cellular events. The understanding of its regulatory role requires the discovery of the proteins involved in these processes and how, where and when protein phosphorylation takes place. Investigation of the phosphoproteome of a cell is becoming feasible today although it still represents a very difficult task especially if quantitative comparisons have to be made. Several different experimental strategies can be employed to explore phosphoproteomes and this review will cover the most important ones such as incorporation of radiolabeled phosphate into proteins, application of specific antibodies against phosphorylated residues and direct staining of phosphorylated proteins in polyacrylamide gels. Moreover, methods to enrich phosphorylated proteins such as affinity chromatography (IMAC) and immunoprecipitation as well as mass spectrometry for identification of phosphorylated peptides and phosphorylation sites are also described.

scholarly journals Combinatorial native MS and LC-MS/MS approach reveals high intrinsic phosphorylation of human Tau but minimal levels of other key modifications

2020 ◽  
Author(s):  
Friedel Drepper ◽  
Jacek Biernat ◽  
Senthillvelrajan Kaniyappan ◽  
Helmut E. Meyer ◽  
Eva Maria Mandelkow ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Native Mass Spectrometry ◽  
Eukaryotic Cell ◽  
Cell System ◽  
Mass Spectrometry Analysis ◽  
Phosphorylation Sites ◽  
Spectrometry Analysis ◽  
Phosphorylated Peptides ◽  
Tau Aggregation

AbstractAbnormal changes in the neuronal microtubule-associated protein Tau, such as hyperphosphorylation and aggregation, are considered hallmarks of cognitive deficits in Alzheimer disease. Hyperphosphorylation is thought to take place before aggregation, and therefore it is often assumed that phosphorylation predisposes Tau towards aggregation. However, the nature and extent of phosphorylation has remained ill-defined. Tau protein contains up to 85 potential phosphorylation sites (80 Ser/Thr, and 5 Tyr P-sites), many of which can be phosphorylated by various kinases because the unfolded structure of Tau makes them accessible. However, limitations in methods (e.g. in mass spectrometry of phosphorylated peptides, or antibodies against phospho-epitopes) have led to conflicting results regarding the overall degree of phosphorylation of Tau in cells. Here we present results from a new approach, that is based on native mass spectrometry analysis of intact Tau expressed in a eukaryotic cell system (Sf9) which reveals Tau in different phosphorylation states. The extent of phosphorylation is remarkably heterogeneous with up to ∼20 phosphates (Pi) per molecule and distributed over 51 sites (including all P-sites published so far and additional 18 P-sites). The medium phosphorylated fraction Pm showed overall occupancies centered at 8 Pi (± 5 Pi) with a bell-shaped distribution, the highly phosphorylated fraction Ph had 14 Pi (± 6 Pi). The distribution of sites was remarkably asymmetric (with 71% of all P-sites located in the C-terminal half of Tau). All phosphorylation sites were on Ser or Thr residues, but none on Tyr. Other known posttranslational modifications of Tau were near or below our detection limit (e.g. acetylation, ubiquitination). None of the Tau fractions self-assemble readily, arguing that Tau aggregation is not promoted by phosphorylation per se but requires additional factors.

mzRecal: universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants

2021 ◽  
Author(s):  
Rob Marissen ◽  
Magnus Palmblad
Keyword(s):  
Mass Spectrometry ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Physical Principles

Abstract Summary In mass spectrometry-based proteomics, accurate peptide masses improve identifications, alignment and quantitation. Getting the most out of any instrument therefore requires proper calibration. Here, we present a new stand-alone software, mzRecal, for universal automatic recalibration of data from all common mass analyzers using standard open formats and based on physical principles. Availability and implementation mzRecal is implemented in Go and freely available on https://github.com/524D/mzRecal. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CROP: correlation-based reduction of feature multiplicities in untargeted metabolomic data

2020 ◽  
Vol 36 (9) ◽  
pp. 2941-2942 ◽  
Author(s):  
Štěpán Kouřil ◽  
Julie de Sousa ◽  
Jan Václavík ◽  
David Friedecký ◽  
Tomáš Adam
Keyword(s):  
Mass Spectrometry ◽  
Graphical Representation ◽  
High Resolution Mass Spectrometry ◽  
Mass Spectrometry Analysis ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Spectrometry Analysis ◽  
Metabolomic Data ◽  
Pairwise Correlations ◽  
Resolution Mass

Abstract Summary Untargeted liquid chromatography–high-resolution mass spectrometry analysis produces a large number of features which correspond to the potential compounds in the sample that is analyzed. During the data processing, it is necessary to merge features associated with one compound to prevent multiplicities in the data and possible misidentification. The processing tools that are currently employed use complex algorithms to detect abundances, such as adducts or isotopes. However, most of them are not able to deal with unpredictable adducts and in-source fragments. We introduce a simple open-source R-script CROP based on Pearson pairwise correlations and retention time together with a graphical representation of the correlation network to remove these redundant features. Availability and implementation The CROP R-script is available online at www.github.com/rendju/CROP under GNU GPL. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals KmerFinderJS: A client-server method for fast species typing of bacteria over slow Internet connections

2017 ◽  
Author(s):  
Jose Luis Bellod Cineros ◽  
Ole Lund
Keyword(s):  
Bacterial Species ◽  
Source Code ◽  
Supplementary Information ◽  
The Internet ◽  
Supplementary Data ◽  
Client Server ◽  
Link Type ◽  
Genome Data ◽  
Speed Up ◽  
Internet Connections

AbstractMotivationKmerFinder is a program based on K-mer statistics for identifying bacterial species in whole genome data, that as a web server that have been used more than 10.000 times. Kmer-FinderJS is a development of the KmerFinder that benefits from the downsampling of data using a prefix filtering used by KmerFinder, to minimize amount of data that needs to be transferred between the client and the server.ResultsKmerFinderJS replaces the python based hash structure for holding the databases with a true Key-value database. These improvements are shown to lead to a many-fold speed up of species identification with the internet transfer speeds that are realistic to expect today. It is also shown that the method can find the true content of an artificial metagenomic cocktail with no false positives.AvailabilityThe method is freely available at https://cge.cbs.dtu.dk/services/KmerFinderJS/ and as a source code at https://bitbucket.org/genomicepidemiology/[email protected] informationSupplementary data are available at biorxiv online.

Sign in / Sign up

Export Citation Format

Share Document