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.
- 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.
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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.
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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!
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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.
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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.
- 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.
- 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.
- 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.




Progenesis LC-MS provides detailed control over the quality of the alignment. The integration of database search results for peptide identification into the quantitative dataset is very convenient including MSMS spectra annotation.