ProSightPD Frequently Asked Questions

While some users are still operating ProSightPC on their computers, Proteinaceous has discontinued service to ProSightPC. As of 2018, we are no longer providing software updates ProSightPC software and only offering limited customer service support for this software. We recommend that users migrate over to ProSightPD, which is currently housed in the Proteome Discoverer environment. Existing ProSightPC users can upgrade to ProSightPD (with Proteome Discoverer BASE) for a reduced price.

ProSightPC is our standalone software application. ProSightPD is our set of nodes for performing top down searches in the Thermo™ Proteome Discoverer™ software framework. (Hint: the PD in ProSightPD stands for Proteome Discoverer.)

We offer discounted upgrades to ProSightPD for ProSightPC customers. Please contact your local Thermo™ Sales Rep.

Yes, please download the installer from here. You can then use this license key 7U33-1M9H-BFBD-LF17 to upgrade a previous permanent license.

Our latest release of ProSightPD is version 4.1, which is compatible with Proteome Discoverer version 2.5. We do recommend upgrading to ProSightPD 4.1, as database management is now integrated into ProSightPD 4.1 through Protein Annotator. This new integration means users no longer need to make databases in ProSightPC for use in ProSightPD. In addition, ProSightPD 4.1 now features proteoform quant!

Both ProSightPD 4.0 and 4.1 will work with PD 2.5. Note that you can have more than one version of PD installed on your computer for those users who may have an older license for Proteome Discoverer but would like to use the most recent version of ProSightPD.

We do! ProSightPD™ 4.1 can be downloaded from the Thermo Software Portal. A 60-day demo license is automatically included with the installer. For researchers using any version of ProSightPD before version 4.1, make sure that Proteome Discoverer 2.5 is installed on your computer with an active license (either permanent or demo) prior to installing the third party nodes.

To learn more about our tools, go to our Explore Software page. TDValidator is available for a 90-day free trial before purchase. Please contact us for the trial license and installer. TDViewer can be downloaded without a license from the NRTDP website. ProSight Lite can be downloaded without a license as well.

Yes, you can download it here.

See Resources>Databases here.

Yes, you can. ProSightPD 4.1 comes with the kDecon algorithm for charge state deconvolution. kDecon was developed to detect protein masses from data where isotopes are unresolved (e.g., Orbitrap spectra with 7500 or 15000 resolving power). kDecon can be used in ProSightPD by selecting the kDecon Med/High cRAWler.

Yes, you can. Use our subsequence search (named Biomarker in ProSightPC and early versions of ProSightPD) to look for protein truncations or clipping products of therapeutic proteins.

FASTA file formats are supported in ProSight. However, we do not recommend using them as no mods will be incorporated into your search. ProSight uses the annotations in .xml files to determine the candidate proteoforms that will be searched against. Because FASTA files have no annotations in them, no modifications will be present to search against. If you only have a FASTA file available, you can upload FASTA files into either ProSight Annotator in ProSightPD or our standalone ProSight Annotator tool to manually curate accession numbers with modifications.

This node ‘crawls’ through a RAW file, grouping MS2 scans together based on user-defined precursor target ion m/z and retention time tolerances. MS1 scans are also grouped and summed according to the MS2 groupings found. These MS1 and MS2 groups are then processed with deconvolution algorithms. For high-resolution data, Xtract is used for both precursor and fragmentation mass detection. For medium resolution precursor data, ReSpect or kDecon is used depending on the cRAWler node chosen. Note that high resolution data is always required for fragmentation scans as Xtract is the only option. Xtract only works with isotopically resolved data.