Genome-based peptide Fingerprint Scanning (GFS) maps peptide mass fingerprints (PMFs), along with tandem mass spectrometry (MS/MS) data when available, or Shotgun MS data directly to genomic sequence, either raw or annotated. The program can enable identification of proteins in genomes for which annotation is lacking, and can identify annotated genes when possible. Welcome to the web interface of the Giddings Lab's GFS service. There are other public interfaces to GFS; you are at the main GFS website. GFS is open-source software, freely available for major operating systems.
You can match and score your MS data to genomic loci in two main modes, with many variations. The main modes are:
- PMF: Peptide Mass Fingerprint, with or without tandem MS (MS/MS) data (Fingerprint tab at left)
- Shotgun: '.pkl' or '.dta' files can be used (Shotgun tab at left)
- Click the Fingerprint or Shotgun tab at left at any time, to submit data in either mode.
Welcome to the GFS Version 2 website. Please note:
- this site, and indeed its underlying GFS code, are updated on a regular basis, including:
- the hardware (see New Hardware below);
- the GUI interface to GFS's many capabilities;
- the genomes and annotations available for searching on this site (see below);
- and of course the underlying GFS code.
- As such, we occasionally have restarts and downtime. We try to keep it brief, and infrequent. We thank you for your patience, and encourage you to contact us with any issues regarding this website's handling of your data.
- while not every error can be accounted for (e.g. if your input file has improper formatting), we continue to improve our automatic error reporting system, and always welcome your feedback.
If you have any of the following needs, please request your own copy of GFS so that others may share our web-based resources equally:
- if you have very large shotgun datasets, and/or many experiments to run.
- if our website does not currently include your genome (you can request that we add it -- note that we are working on uploadable genomic sequence, and that ~60 new genomes are coming online soon).
- if you are working with confidential data: this website is not secure, and all GFS results are always e-mailed (see next item).
- if your analyses take a long time (sometimes hours). Many users need to submit their test data and parameters, then close their web browsers, which is often in fact wise. For this rceason, all GFS results are always e-mailed, and are also presented onscreen if your browser window is still open.
New hardware has just arrived that will support more web jobs; your patience is appreciated while we iron out all the wrinkles. Your job will start immediately, but the time for results varies depending on the complexity of your experiment and any other experiments that you are sharing our computers with. Many short jobs compute in seconds, e.g. a short PMF against E. coli), while others, e.g. a full set of shotgun spectra against a large genome, take too long to stay awake for. In such cases, you should run GFS on your own machines (see Request link above).
- Known Issues:- If you want to resubmit a job, or you cancel a job, or there is an error: some of your previous input values may need adjustment. Make sure all your parms are noted, and your input data are correct, before you submit your data, and whenever you resubmit. We currently preserve some of these values during your worksession, but not all (we are improving this data persistence).
- T. thermophila searches are currently contained to annotated gene sequences, not full genome.
