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by Matt Schnell | Mar 24, 2023 | ProteinPilot, Proteomics, QTOF, Questions
Hello,
by Roz Jenkins | May 25, 2022 | Data processing, Life Science Research, ProteinPilot, Proteomics, QTOF, Questions
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
by Adrian Brown | May 12, 2022 | Data processing, ProteinPilot, Proteomics, QTOF, Questions
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?
by Alexandra Antonoplis | Aug 11, 2021 | Data processing, Life Science Research, OneOmics, ProteinPilot, Proteomics, SCIEX information
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...
by Christie Hunter | Aug 6, 2021 | Data processing, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF
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...
by Christie Hunter | Aug 6, 2021 | Data Visualization, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF
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...
by Alexandra Antonoplis | Aug 6, 2021 | Data Visualization, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF
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...
by Alexandra Antonoplis | Aug 6, 2021 | Data processing, Life Science Research, OneOmics, ProteinPilot, Proteomics, SCIEX information
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...
by Christie Hunter | Aug 6, 2021 | Data processing, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF
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...
by Christie Hunter | Aug 6, 2021 | Data processing, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF
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...