Monday, July 29, 2013

FDR on combined result from multiple search engines

There are many database search software available for peptide identification. Every software use different scoring functions, thus give them complementary abilities in assigning different spectra from the same MS/MS dataset. This makes combining multiple search engine results a popular methods among researchers.

The tricky part when dealing with the combined results is how to control the quality. In PEAKS 6, we introduced a very easy to use filter in the inChorus result to help resolving this issue. To use this feature, 'Search decoy database from PEAKS' option must be selected for individual search engines when performing inChorus search.

In the 'inChorus' summary view, there is a 'Edit filters' button to control the FDR at the PSM level.

Click the button, a dialog with filter details will be displayed.

The easiest way is to select the target inChorus FDR and PEAKS will automatically determine the appropriate score threshold for each individual search engine so that the combined result has the FDR the user specified. PEAKS also gives users the flexibility to select the score threshold for individual engines manually. When the filters are applied, the overall FDR of the combined result will be calculated.

Tuesday, July 16, 2013

PEAKS performs excellently on AB SCIEX TripleTOF 5600 data

AB SCIEX TripleTOF 5600 is a powerful instrument that provides high mass accuracy and high resolution in both MS and MS/MS modes. With the ability to acquire a maximum of 50 MS/MS spectra per second, the instrument makes a great component for a proteomics research platform.

PEAKS algorithm has been optimized specifically for this type of instrument in version 6. A comparative study was performed using iPRG 2012 dataset against Mascot and ProteinPilot. The results are shown in the following table.

At 1% FDR, PEAKS 6 was able to identify twice as many PSMs as the popularly used Mascot + Percolator combination. Even compared with AB SCIEX’s ProteinPilot software, PEAKS 6 identified 29% more PSMs.

*The content of this post is extracted from ASMS 2012 poster "Optimized Database Search Software for Peptide Identification with AB SCIEX TripleTOF 5600". You can find a copy of the poster here.

Thursday, July 4, 2013

How to use Decoy-Fusion on Mascot in PEAKS inChorus?

PEAKS supports FDR estimation on inChorus results. To make this work on Mascot results, there are a few extra steps to follow.

PEAKS uses Decoy-Fusion method for FDR estimation. The first step is to create a decoy-fusion database. Go to PEAKS database configuration dialog. Select the FASTA database you want to search against. Then click the "Export Decoy DB" button. A decoy-fusion FASTA file will be generated.

The second step is to configure the decoy-fusion FASTA file into Mascot. This is very straightforward in Mascot 2.4 as the parsing rule of PEAKS decoy-fusion method can be automatically detected.

After the decoy-fusion database is up and running on Mascot server, the last step is to make sure that the "Search decoy database from PEAKS" option is selected in the search dialog.