The newest release of Sorcerer Proteomics Edition (Sorcerer PE) software is now available in beta to supported Sorcerer customers. It introduces several new enhancements:
- New native file formats based on MS2 and SQT for greater data handling efficiency
- The obsolete DTA and OUT formats have been removed from the internal flows of Sorcerer but are still available for import and export to legacy applications
- Improved system performance and efficiency throughout.
- Support for the multiple biosample feature of Scaffold — spectra files can be pre-grouped in the search to become separate biosamples in the Scaffold file
- Built-in processing for Raw files from Thermo LTQ Orbi Velos and Q Exactive mass spectrometers
- Now bundles the most recent TPP 4.5.2 software
- Support for Scaffold V3.4
Release 4.2 is the latest in the V4 series of Sorcerer Proteomics Edition (Sorcerer PE) software, and is immediately available for beta testing, which means that all the new features have now been implemented and tested internally, but that the software has not yet received full testing in real-world conditions. If you would like to try out the new features, then please contact firstname.lastname@example.org to request the new beta software. If you are currently using version 3.5 or earlier releases, you will also need to enter new license keys.
Sorcerer PE V4′s NEW FILE formats OFFER greater PERFORMANCE
This release completes the transition to new file formats that was begun with v4.1 (which still used the old formats behind the scenes), and now all of Sorcerer PE’s internal use of the legacy Sequest DTA and OUT file formats has been replaced by the more modern MS2 and SQT formats for representing MS2 spectra and peptide matches respectively. In these days in which tandem mass spectrometers can generate tens of thousands of spectra every hour, it is very inefficient to represent each data item in a separate file — there is a substantial overhead in opening and closing each file, and transfers in a network environment such as Sorcerer uses are typically slow. It also wastes a lot of disk space. So using MS2 and SQT natively throughout the Sorcerer search engine greatly improves the overall performance of the system.
However, although they work well internally to the system, we don’t recommend these formats for an end-user to work with directly — the formats are neither standardized, amenable to upstream and downstream processing tools, nor easily generalized to other search algorithms. Rather, for input to and output from Sorcerer, we’ve standardized on mzXML for spectra and pepXML for peptide matches as interchange formats that are more general and with extensive community support. PepXML is now generated by default, even if you do not select TPP postprocessing overall. Of course, Sorcerer supports other formats, too, such as Thermo’s Raw files, but these will be converted to pass through the standard formats — mzXML in the case of Raw files.
One more word about DTA and OUT file legacy support: these files are no longer directly supported by the Sorcerer PE search engine, but you can still import DTAs, and we will have a script to generate OUT files from pepXML, if your downstream processing requires them. Please note that there is one spot in the TPP suite that expects .out files, and that is the “spectrum” hyperlink in the Peptide Viewer, which actually brings up a view of the out file, if any. Most of the scores, masses etc. for the spectrum match that are presented in that view can be added as columns directly to the peptide report. But if you do want to view these OUT files and you don’t mind the extra overhead, then consider running the OUT file compatibility script as a post-processing step. Please consult email@example.com for further assistance with the compatibility script.
Multiple Biosample support for Scaffold
One common request from our clients who are keen Scaffold users is for enhanced support in the Sorcerer-Scaffold integration that can take advantage of Scaffold’s ability to group data into different biosamples, corresponding to different columns in the Scaffold view. We’re happy to announce a new feature in the Sorcerer PE software that speaks to this. The way it works is very simple, and requires only a minor difference to the way you have always searched data on Sorcerer.
Previously, if you selected multiple items for searching in the Web GUI, they would all be searched together and would wind up being a single biosample in the Scaffold file. Now, any separately selected item — either a single spectra file, or a folder of several files — will become its own biosample. Typically, the way this is used is to pre-group raw files in subfolders of the search data folder, and each of those subfolders will become a separate biosample, so long as they are each individually selected from within the search data folder. If, however, you select the search data folder itself at the top level, then all its contents will become a single biosample.
Of course, the existing method of working with Scaffold Desktop to add new biosamples based on merging with another Scaffold file is still available, so you can choose whichever method is more suitable for your needs.
Do be aware though, that searching more data in one run will add to the load of the Scaffold analysis. The system resources that Scaffold needs, particularly in terms of memory, is a function primarily of the number of files, and the number of spectra represented by those files. We recommend that any Sorcerer that is used for intensive Scaffold analysis should be upgraded to a minimum of 24GB of system RAM, and that users should discuss their Scaffold analysis usage and possible upgrades to their system with Sage-N support in order to ensure the best performance.
New method for extracting Thermo RAW files in Sorcerer
When Thermo introduced XCalibur 2.1 and 2.2 supporting the Orbi Velos and Q-Exactive instruments, incompatibilities in their libraries meant that the method of extracting spectra from Raw files that Sorcerer then used suddenly stopped working. In response to this, Sage-N Research developed a solution based on a new software method, but that was Windows-specific, and not well suited to other platforms such as Linux. Nevertheless, at the cost of some complexity, particularly in terms of installation, we made it work on Sorcerer, and once again had an integrated flow with Sorcerer PE for XCalibur 2.1 and above.
Now we have implemented an alternative approach, based on a method developed by Dr. Patrick Pedrioli at the University of Dundee, that allows that Sorcerer’s built-in extraction software to be used successfull with the latest XCalibur libraries. It is a lot easier to deploy on Sorcerer than the Windows-based solution , and just requires a few tweaks that Sage-N customer support can easily guide you through or do remotely. This method is now the default flow for the Sorcerer PE 4.2 release.
The Windows/msconvert method remains available for qualified customers who have the requirement to use its different feature set.
New versions of TPP and ScaffolD Software
The version of the bundled Trans-Proteomics Pipeline (TPP) software has been updated to the most recent 4.5.2 software, which provides several new enhancements and bug fixes. Also, the most recent version of Scaffold, V3.4, is now supported. Licensed users may obtain this software at the Proteome Software download site.
Other Sorcerer PE V4 enhancements
The new release rolls up other enhancements from earlier V4 releases including:
- The SEQUEST 3G scoring module with new features to improve the sensitivity and thoroughness of peptide searches.
- A new Web API for submitting and getting results from Sorcerer searches over the network has been implemented to help developers use Sorcerer as a search engine within their programs and scripts.
- A component design for the Sorcerer-as-a-platform architecture, co-existing with other life science analysis software
- Enhancements to the MUSE scripting framework to allow more powerful scripts to customize Sorcerer searching.
Please review an earlier posting for further details of these and other enhancements in Sorcerer PE V4.