Both PEAKS de novo and PEAKS DB search were finished successfully on the 3.4 million MS2 dataset. The computer has two Xeon hex-core CPUs and 32GB RAM running Windows 7 Pro 64 bit OS. The search completed in a little over a week.
PEAKS de novo reported over 2 million de novo peptides that have their ALC score greater than or equal to 50%.
PEAKS DB reported over 1 million PSMs at 1% FDR.
Be sure to check out the protein coverage view of one of the top score proteins. It can help demonstrate that a protein is pretty much fully covered.
Showing posts with label Summary View. Show all posts
Showing posts with label Summary View. Show all posts
Saturday, April 6, 2013
Tuesday, April 2, 2013
A few quick issues of running PEAKS on OS X and Linux
I have played PEAKS as a viewer on a Mac OS X for a while and do notice some minor issues. That's expected as PEAKS on OS X is not officially supported!
No instrument raw file loading ability. This could probably never be fixed unless the instrument vendors port their libraries to OS X. So in short, PEAKS can only read text formats (mgf, mzxml, mzml, pkl, dta, etc) and of course PEAKS projects on OS X.
Images on the summary view is broken. This seems to be a coding issue related to the path (file path on Windows and OS X are different). I do manage to get a workaround though. On the summary view, click "Notes" button on the top of the view, a text editor will show up. Type in the following and click "OK".
Vertical tabs are too small and the text on them are not visible. Well, not sure how to workaround this. But when you mouse over the tabs, the tooltips do work.
I will keep playing PEAKS on OS X when I have chance. Please comment if you find other interesting issues :D
No instrument raw file loading ability. This could probably never be fixed unless the instrument vendors port their libraries to OS X. So in short, PEAKS can only read text formats (mgf, mzxml, mzml, pkl, dta, etc) and of course PEAKS projects on OS X.
Images on the summary view is broken. This seems to be a coding issue related to the path (file path on Windows and OS X are different). I do manage to get a workaround though. On the summary view, click "Notes" button on the top of the view, a text editor will show up. Type in the following and click "OK".
<a href="">go</a>A "go" link will be displayed in the "Notes" section of the summary view. Click on the link, the summary view will be correctly displayed in your default web browser.
Vertical tabs are too small and the text on them are not visible. Well, not sure how to workaround this. But when you mouse over the tabs, the tooltips do work.
I will keep playing PEAKS on OS X when I have chance. Please comment if you find other interesting issues :D
Friday, March 15, 2013
'Experiment Control' is a valuable tool
There are so many factors that can make database search engines fail to produce a decent result. Today I saw such an interesting case.
A user send in a dataset generated from Orbitrap instrument. When he used PEAKS to analyze the data, surprisingly, he only got very few PSMs. I examined the figures in the 'Experiment Control' section in the 'Summary View' and noticed that the precursor mass error distribution of the PSMs is strange. So I increased the parent ion error tolerance from 10ppm to 20ppm and got very good result. One third of the spectrum have been identified under 1% FDR.
The figures in the 'Summary View' sometimes can help identify the problem when the search result is not ideal. In this case, the instrument is not well calibrated.
A user send in a dataset generated from Orbitrap instrument. When he used PEAKS to analyze the data, surprisingly, he only got very few PSMs. I examined the figures in the 'Experiment Control' section in the 'Summary View' and noticed that the precursor mass error distribution of the PSMs is strange. So I increased the parent ion error tolerance from 10ppm to 20ppm and got very good result. One third of the spectrum have been identified under 1% FDR.
The figures in the 'Summary View' sometimes can help identify the problem when the search result is not ideal. In this case, the instrument is not well calibrated.
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