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Frequently Asked Questions

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Anurag Raj edited this page Jul 11, 2023 · 2 revisions

Q: What are the hardware requirements for PgxSAVy?
A: This depends on the number of variant peptides and MS/MS spectra file. In general, we recommend at least 4 GB, but large files will require more. Additional BioAnnotation will require additional memory and hard disk space.

Q: What are the software requirements for PgxSAVy?
A: PgxSAVy is a standalone tool and does not require any additional software. It is written in Perl and can be run on any operating system. It has been tested on Windows, Linux and Mac OS where Perl 5.10 or later is installed. It requires the following Perl modules to be installed: Statistics::Zed (0.10)-- used in zscore estimation, InSilicoSpectro::InSilico::MassCalculator (not required to install, provided with tool).

Q: Do I need to convert raw MS/MS files to MGF file format?
A: Yes, PgxSAVy requires MGF file format for MS/MS spectra. You can use any of the freely available tools to convert raw MS/MS files to MGF format. We recommend ProteoWizard (https://proteowizard.sourceforge.io/).

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