FAQs for Progenesis LC-MS v4.1
System requirements & compatibility
- What PC specification do I need to run Progenesis LC-MS?
- Why is it better to run Progenesis LC-MS on a 64-bit operating system?
- What file formats, data types and instrument types are supported?
- What search engines and databases are supported?
- What inclusion list formats are supported?
- What is new in the latest version? (655KB)
- How can I send my experiment to a colleague or collaborator?
- How has data processing been improved in Progenesis LC-MS v4.1?
- Do you have any tips to make automated data processing more efficient?
- How do I choose an alignment reference?
- Can I still apply a stepwise approach to reference run selection and alignment?
- How does alignment work in Progenesis LC-MS?
- How can I import an experiment design from an external file?
- How does normalistion work in Progenesis LC-MS?
- Do I need to filter out MS1 data to control for outliers and for normalisation to work?
- How does normalisation behave where peptide ions significantly altered in their abundance are derived from proteins which do not express any changes in their abundance?
- Why does Progenesis LC-MS quantify before identifying?
- How do "same peptide" outlines work in Progenesis LC-MS?
- How do I use tags?
- Can I use wildcards when filtering my runs and peptides?
- How are peptide abundances calculated?
- How are protein abundances calculated?
- What are data compression and peak modelling and why do you do this?
- How do I run an MS/MS ion search?
- What does Principal Component Analysis (PCA) show?
- Why should I fractionate my biological samples?
- How do I analyse fractionated biological samples in Progenesis LC‑MS?
- How (& why) should I order my fractions after importing them?
- What is the relevance of the Peptides per fraction chart?
- Why do I need to recombine my fractionated samples in Progenesis LC‑MS?
- How do I use the Recombine Samples page to recombine my fractionated samples?
- How do my experiment designs affect analysis?
- How is normalisation performed in fractionated LC-MS experiments?