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ProteinPilot phosphopeptide library and DIA-NN

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

ProteinPilot phosphopeptide library and DIA-NN

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

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...

Downloading and viewing ProteinPilot app group files on your desktop and extracting key exports

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...