GEN-MKT-18-7897-A
Dec 4, 2015 | Blogs, Life Science Research, Proteomics | 0 comments
A recent webcast by Charles Pineau, Director of Protim, IRSET, Rennes, France, demonstrates how you can use the OneOmics™ Platform as a “Click & Easy” workflow for integrating next-generation proteomics (NGP) data with next-generation sequencing (NGS) data. Dr. Pineau and his colleagues are interested in gaining new insights into human spermatogenesis and understanding the dialogue between germ cells and somatic cells. In previous research using rat samples, over 1400 unannotated transcripts were identified. Subsequent proteogenomic studies then showed that some of those transcripts encoded for novel proteins. The data analysis for that research was performed using the open source EMBOSS suite of tools.
In the current study, the researchers were interested in analyzing human samples and developing a more simplified workflow for data analysis. Using the SCIEX TripleTOF® 6600, and the Illumina HiSeq 2500, over 1100 new potential transcripts were identified with more than 2 peptides at FDR < 1%. The OneOmics Platform was used for data processing and analysis. Compared with the previous open source EMBOSS suite of tools used in the rat studies, the OneOmics Platform was about 75x faster. Additionally, another major benefit using the OneOmics Platform was the relative ease with which the data could be analyzed compared with the previous workflow which required extensive user customization by writing scripts and formatting files. This enabled the researchers to focus on the biology rather than the complications associated with formatting datasets and transformation of files. Ongoing studies are taking a subset of candidates and validating them using MRM studies, qPCR, and immunohistochemistry.
Comment below to get a demo OneOmics today.
Finding the right information shouldn’t slow you down. Whether you’re troubleshooting your mass spec, learning something new, or optimizing performance, access to the right resources at the right moment makes all the difference.
As an analytical strategy, middle-down mass spectrometry (MS) workflows characterize biotherapeutic proteins by analyzing large, digested protein fragments or defined subunits, rather than fully intact proteins (top-down) or digested peptides (bottom-up). A middle-down strategy combines the strengths of top-down and bottom-up approaches by delivering high sequence coverage and structural specificity while maintaining relatively simple sample preparation. In practice, middle-down analysis enables accurate mass measurement, rapid sequence confirmation, and localization of key post-translational modifications (PTMs) on protein subunits that are directly relevant to product quality.
In biopharmaceutical development, sequence variants (SV) are considered an inherent risk of producing complex proteins in living systems. Sequence variants are unintended changes to the amino acid sequence of a biotherapeutic and can be caused by errors in transcription or translation in the host cell, or cell culture and process conditions. Detailed analysis of SVs is important in process and product development to ensure the drug’s safety and efficacy. Even low‑level sequence variants can have significant implications for product quality, safety, and efficacy, making their accurate detection and characterization a critical requirement across development, process optimization, and regulatory submission.
Posted by
You must be logged in to post a comment.
Share this post with your network