Progenesis QI FAQs
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System requirements & compatibility
- What PC specification do I need to run Progenesis QI?
- Why is it better to run Progenesis QI on a 64-bit operating system?
- What instrument types, data types and file formats are supported?
- Which search engines and databases are supported for identifying compounds?
- What inclusion list formats are supported?
- What pathway analysis tools are supported?
Licensing
- What are sample licence codes and how do they work?
- How do I update my dongle to enable analysis in a new version of the software?
Quick start & overviews
- Fundamental concepts in the QI workflow
- How do I update my dongle to enable analysis in a new version of the software?
Recent Experiments screen
- What are the implications of deleting a file from the Recent Experiments list?
- How can I send my experiment to a colleague or collaborator?
- What is the Progenesis Improvement Program?
- How can I backup my experiments?
New Experiment wizard
Import Data screen
- Which file formats are supported?
- My file format isn't listed; how can I import my data?
- What is an ion intensity map?
- Can I begin analysis while my run data is importing?
- What do the “peak count” values mean in the About This Run box?
- How can I assess the quality of my chromatography?
- How do I remove a run from my experiment?
- My runs show far fewer ions than I would expect; what might have caused this?
- Should I remove runs that have been imported with warnings?
- What are masks used for in Progenesis?
- How can I apply the same mask to all runs?
- What does it mean for runs to be “protected from editing”?
- How should I choose my alignment reference?
- How do I carry out automatic processing?
Review Alignment screen
- How does Progenesis correct for drifts in retention time?
- Why is alignment so important?
- What do the visualisations at Review Alignment show?
- How can I align my samples automatically?
- How should I choose my alignment reference?
- What is an alignment vector?
- How do I review and edit the alignment of my runs?
- How do I manually align runs that fail to align automatically?
- How can I correct localised alignment errors?
- How can I prevent my manual vectors snapping to the wrong location?
- How can I zoom to an area in the Review Alignment screen?
Experiment Design Setup screen
- How do my experiment designs affect analysis?
- Do I need to include all runs in each of my experiment designs?
- How do I analyse a mixture of technical and biological replicates?
- Can I import my experiment designs from an Excel file (or other file)?
Peak Picking screen
- Which runs should I use for peak picking?
- How can I detect more ions in my samples?
- How can I edit the results of peak picking?
- How can I avoid peak-picking the contaminants, salt-front, etc. in my samples?
Review Normalisation screen
- How does normalisation work in Progenesis?
- Do I need to filter out MS1 data to control for outliers and for normalisation to work?
- How do I perform normalisation using an external standard?
Review Deconvolution screen
- How do I use the Review Deconvolution screen?
- How are compound ions grouped into compounds?
- What does the grid in the top half of the Review Deconvolution screen show me?
- How can I use the mass profile and chromatogram to review deconvolution?
- How do I edit the set of ions from which a compound is formed?
Identify Compounds screen
- Which search engines and databases are supported for identifying compounds?
- How does the MetaScope search engine work?
- What columns should my Excel file contain for use as a compound database in MetaScope?
- What are fragment databases and how do I use them?
- Why is fragmentation data required to be in a separate file?
- How can I use MSMS or MSá´± information to improve my compound identifications?
- How can I create my own mass spectral databases?
- What are additional properties files and how do I use them?
- How can I use ion mobility data to improve my compound identifications?
- How can I annotate my compound databases with CCS values?
- Can I combine compound identifications from multiple sources?
- How are the scores calculated for possible compound identifications?
- How is the fragmentation score calculated for possible compound identifications?
- How does the theoretical fragmentation work?
- How does database fragmentation scoring work?
- How do I use the fragmentation graphs?
- How can I see the search parameters that were used to produce my compound identifications?
- What do the letters represent in the Score column of possible identifications?
- How do I decide which compound identifications are correct?
- What's the significance of accepting identifications?
- How can I reject possible compound identifications?
- How can I get more identifications using inclusion lists in Progenesis?
Review Compounds screen
- How can I validate my compounds?
- Why are none of the compounds I export being found in my pathways analysis?
- Should I use enrichment or over-representation analysis for pathways data?
- How do I export compound data to EZinfo, and import results back from EZinfo into Progenesis QI?
- Why has my copy of EZinfo stopped working since I purchased Progenesis QI?
Compound Statistics screen
- What does Principal Component Analysis (PCA) show?
- What does the dendrogram show, or what is correlation analysis?
- What are p-values?
- What are q-values, and why are they important?
- What is power analysis?
- What is the difference between standardised and normal abundance expression profiles?
General analysis and productivity
- How can I show only the interesting compounds?
- How can I quickly show a known location in the ion intensity maps?
- Can I use wildcards to filter runs and compounds?
- What is the Clip Gallery and how do I use it?
- How do I export compound data for external analysis?
- How can I get more identifications using inclusion lists in Progenesis?
Algorithms
- What are data compression and peak modelling and why do you do these?
- How are retention times automatically aligned across runs?
- How does normalisation work in Progenesis?
- How are compound ions grouped into compounds?
- How are the ion measurements calculated?
- How are the compound measurements calculated?
- Why are compound measurements stabilised?
- How are the scores calculated for possible compound identifications?
- How does the theoretical fragmentation work?
- How does database fragmentation scoring work?