Evidence Progenesis LC-MS works

Here are examples, from Progenesis LC-MS users and our own work, demonstrating how the software can add real benefits to your quantitative label-free LC-MS proteomics research.

1. Label free LC-MS analysis for integrated preclinical pharmaceutical toxicology. Using Progenesis LC-MS, University College Dublin, achieved excellent analytical reproducibility and good proteome coverage, with modest instrument time per sample.
   
   
2. Analysis of membrane proteins, with targeted inclusion lists to increase proteome coverage. Dept of Protein Science Helmholtz Center Munich used Progenesis LC-MS to find membrane proteins involved in progression of an incurable autoimmune disease. The number of identified proteins, that were differentially expressed, was increased in a targeted way using inclusion lists of peptides missing fragmentation generated by the software.
   
   
3. Fast, accurate, objective protein quantification and identification. Dr. Alexander Ivanov at the Harvard School of Public Health in Boston challenged us to quantify and identify 9 proteins, present in different relative amounts between 2-1000 fmol, using Progenesis LC-MS. The challenge was that we didn’t know which proteins were present and what their relative concentrations were. Progenesis LC-MS identified them all!
   
   
4. Applying a low resolution ion trap instrument to label-free LC-MS quantitative proteomics. Data from Professor Gary Black and PhD student Andrew Porter showed how Progenesis LC-MS enables you to visualise complex MS data and optimise quantification of a complex protein mixture using a low-resolution ion trap MS instrument coupled to uHPLC.
   
   
5. How to reliably infer protein expression changes from peptide ion measurements. How Progenesis LC-MS performs this key step and the advantages the approach gives to reliably measuring relative protein expression. This technical note also includes published evidence demonstrating the accuracy and reliability of protein quantification by Progenesis LC-MS.
   
   
6. Save time handling complex samples. Sample run times can be long; a 40 fraction offline separation strategy can require >5 days to run and analyse. Progenesis LC-MS quantifies complex label-free protein samples, which can remove or reduce the need for pre-fractionation steps. This saves instrument time and minimises the effects of instrument drift or failure between runs.
   
   
7. Discover protein behaviour you may have missed with traditional approaches. You can quickly analyse high numbers of biological and/or technical replicates with no missing data using Progenesis LC-MS. This generates data for valid multivariate statistical analysis, leading to significant expression differences that you can report with confidence.
   
   
8. A quantify-then-identify approach to label-free LC-MS data analysis. Progenesis LC-MS applies a new approach to quantify and then identify differentially expressed proteins as rapidly, objectively and reliably as possible.