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.
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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.
CE‑SDS remains a cornerstone assay for characterizing fragmentation, aggregation, and product‑related impurities in therapeutic proteins. UV detection has been the long‑standing standard. However, it frequently struggles with baseline noise, limited sensitivity for minor fragments, and subjective integration.
At SCIEX, innovation doesn’t stop at instruments; it extends to how you interact with your LC-MS/MS or CE systems every day. That’s why we’re excited to introduce the SCIEX Now spring 2026 improvements: a set of meaningful enhancements shaped directly by your feedback.
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