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ProteinPilot
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ProteinPilot phosphopeptide library and DIA-NN
I have prepared a spectral library for a phosphopeptide enriched sample and I am generating my SWATH samples from similarly enriched samples. The problem is that when I use DIA-NN for the retention time alignment and quant, it doesn’t recognise the terminology of the spectral library annotated by ProteinPilot. DIA-NN recognises Unimod:21 for phosphorylation, but PP uses phospho(Tyr) etc. Other than changing the data dictionary to get around the mismatch, anyone have any suggestions for how I might resolve this? Thank you, Roz
Sequential processing of multiple data-files in ProteinPilot
I would like to use ProteinPilot 5.0.2 to process data-sets containing 16 wiff files acquired from fractionated peptides on a 6600 TripleTOF. A Precision T7910 workstation struggles to process four files in parallel and I would like to be able to queue sequential processing of individual files overnight. I currently use the ‘LC ‘ tab to load and process individual data-files but this leads to parallel processing. Is it possible to generate 16 .group files sequentially?
Merging two FASTA files
There is an easy way to merge two FASTA files together. Open notepad and type this string: type %*>"newfile.fasta" Enter any name for the FASTA file between the quotes. Save the file as: Merge FASTA files.bat Copy the two files you want to merge into the same...
What is the difference between the gobal and the local FDR rates in ProteinPilot software?
The main idea of the target-decoy approach to compute false discovery rates is to feed the search engine answers that you know are wrong. These are referred to as ‘decoys’, typically generated by reversing, randomizing, or scrambling real protein sequences. You then...
Protein alignment template for results comparisons across multiple group files from ProteinPilot software database searches
The key challenge in aligning protein level results is flexible matching by making use of the accession ambiguity in reported protein groups. The better this task is done, the more complete will be the protein matching across multiple results. For quantitative work, a...
How do I use the new ProteinPilot software reports (small vs large)?
At the end of a database search, the software will write information into the ProteinPilot Report automatically. The ProteinPilotReport.xlsx file must be placed in the following directory for the automatic creation to work. C:\Program Files\AB...
Downloading and viewing ProteinPilot app group files on your desktop and extracting key exports
After the database search in OneOmics suite, the ProteinPilot software group file can be downloaded for viewing in your desktop ProteinPilot software 5.0.3. Once downloaded, you can open and view your Group file in the ProteinPilot software as usual. You can also now...
Understanding MS1 Peak Intensity in ProteinPilot software
The “Intensity (Peptide)” values come from LCMSReconstruct, in ProteinPilot software 5.0. It maps the RT, m/z, intensity MS1 surface to find the peak information for the peptide. The Intensity (Peptide) is a weighted sum of the heights of the isotope series at the...
What is the difference between a rapid and a thorough search in ProteinPilot software?
When setting up your search in ProteinPilot software, you select either a Rapid Search or a Thorough Search in the Search Effort section. This setting determines which parts of the algorithm will be invoked and effectively how deep into your sample you will search to...
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