ProteoSign: an end-user online differential proteomics statistical analysis platform

Abstract

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a user-friendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ProteoSign.

Calcitriol Supplementation Causes Decreases in Tumorigenic Proteins and Different Proteomic and Metabolomic Signatures in Right versus Left-Sided Colon Cancer

“…A reverse sequence database was used to search the peptides to determine the false discovery rate (FDR) set to 0.01. iTRAQ 8-plex was used as the reporter ion quantitation type as well as instrument Orbitrap MS and MS/MS. Further data analysis was performed with ProteoSign, a web-based software for differential protein analysis [ 46 ]. Functional classification was performed using Ingenuity Pathway Analysis (IPA).…”

ProtExA: A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics

“…The BLM is a well-evaluated methodology adequate to provide statistically stable results for any kind and for any pair of numeric populations of values, even for very small data sets. The underlying method has been recently used by Efstathiou et al [2] , on protein expression datasets with trustworthy results. Further to the above mentioned imputation schemes, ProTExA further provides a series of data normalization methods, as well as the ability to perform logarithmic transformation on the dataset under study, prior performing the LIMMA statistical package.…”

“…Current state-of-the-art tools for biomarker and pathway discovery have been mostly focused on the analysis of genomic and transcriptomic datasets, as opposed to proteomics software workflows [1] . Such tools although they provide significant information about the quality and biological variability of proteins-genes and their expressions across different samples, they are limited to the processing and statistical visualisation of raw data, as well as to the identification-quantification of proteins [2] , [3] , [4] . Existing pipelines for protein and gene expression data analysis [5] , can be found in separate tools which in effect make almost impossible for someone without having a least of software development skills, to construct an overall analysis framework that leads to biomarker and pathway identification [6] , [7] .…”

Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses

“… 57 ProteoSign is based on LIMMA and works with TMT, stable isotope labeling with amino acids in cell culture (SILAC), and iTRAQ. 58 DeqMs, designed for TMT, is based on log2 normalization and LIMMA. 59 Isobar is an R package designed for TMT and iTRAQ.…”