The PPP-labels software for quantitative proteomics
Lead Research Organisation:
University of Liverpool
Department Name: Institute of Integrative Biology
Abstract
The large-scale study of proteins (the functional molecules in cells) is called proteomics and the main technology for identification and quantification is mass spectrometry (MS). There are two popular proteomics methods, called "label-based" and "label-free". One of the leading commercial software packages for label-free data analysis is Progenesis LC-MS from Nonlinear Dynamics (Newcastle, UK). We previously developed an application for adapting Progenesis LC-MS to analyse data from label-based studies, called the Progenesis Post-Processor (PPP). In this project, we are in the process of commercialising this software in a product called PPP-labels. We have requested support in the lead up to the release of the first version on the open market. We are also going to generate data sets in which we know the abundance of proteins to demonstrate and benchmark PPP-labels.
Organisations
Publications
Carr DF
(2017)
Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population.
in The Journal of antimicrobial chemotherapy
Ghali F
(2016)
Proteome Informatics
Ghattaoraya GS
(2016)
A web resource for mining HLA associations with adverse drug reactions: HLA-ADR.
in Database : the journal of biological databases and curation
Ghattaoraya GS
(2017)
Human leucocyte antigen-adverse drug reaction associations: from a perspective of ethnicity.
in International journal of immunogenetics
Gonzalez-Galarza FF
(2018)
Allele Frequency Net Database.
in Methods in molecular biology (Clifton, N.J.)
Gonzalez-Galarza FF
(2020)
Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools.
in Nucleic acids research
Jones A
(2016)
Proteome Informatics
Jones AR
(2020)
Proteome Bioinformatics Methods for Studying Histidine Phosphorylation.
in Methods in molecular biology (Clifton, N.J.)
Peffers M
(2017)
Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data
in Wellcome Open Research
Ramsbottom KA
(2020)
Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles.
in PloS one
| Description | We have developed new software for mass spectrometry data analysis called Proteolabels. Proteolabels is able to perform label-based quantitative proteomics analysis (SILAC, dimethyl-labelled approaches), and functions as a module for the Progenesis QI for proteomics (Waters Corp.) software. Proteolabels has novel approaches for converting peptide quantitative values into protein-level values, and a unique approach for using novel data types for quality control, including ion mobility-MS, which to our knowledge has never before been incorporated into label-based quantitative software. |
| Exploitation Route | The software has been licensed and is available for labs to purchase, as an additional module for popular software Progenesis QI for proteomics. |
| Sectors | Healthcare,Pharmaceuticals and Medical Biotechnology |
| URL | http://www.omicanalytics.com/products/proteolabels/ |
| Description | We have developed commercial software called Proteolabels, which has been licenced to start-up company Omic Analytics who have an exclusive sales and distribution contract for Proteolabels with instrument manufacturer Waters Corp. |
| First Year Of Impact | 2016 |
| Sector | Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Title | Proteolabels |
| Description | Proteolabels is software for SILAC-style quantification in proteomics. The software has been licenced from University of Liverpool to Omic Analytics Ltd. for further develop and support. The software is onward licenced to Waters Corp for internatinoal sale |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Impact | The software has been licenced to start-up company, and is now being sold internationally by Waters Corp. |
| URL | http://www.omicanalytics.com/products/proteolabels/ |
| Company Name | Omic Analytics Ltd |
| Description | Omic Analytics develops products and services in multi-omics and computational biology. |
| Year Established | 2014 |
| Impact | Omic Analytics (OA) has licenced the Proteolabels software from the University of Liverpool, and has a resale agreement in place with Waters Corp. OA is also offering innovative services in omics and computational biology, to a variety of customers. |
| Website | http://www.omicanalytics.com/ |