2013 will come to the end in a few days. It's been a great year for us, the PEAKS team, at BSI and we want to take this opportunity to wish everyone a Merry Christmas and a Happy New Year!
Monday, December 23, 2013
Wednesday, December 18, 2013
Navigate through your LCMS data in PEAKS
PEAKS 7 is released with a re-engineered LCMS view. Users may use this integrated and interactive view to navigate and dig into the data and result easily. In this post, I am going to talk about the controls and functionalities we have built into this view.
The LCMS view can be found on any opened data nodes, identification results and label free quantification results. It contains four main components: the main heatmap view, the control panel, the TIC and the thumbnails.
The 1:1 button (2) will immediately zoom out in the view to display the full heatmap. You can also invoke this function by double clicking your left mouse button anywhere in the heatmap.
The 3D button (3) toggles the view between heatmap and 3D mode. While the heatmap mode is sufficient in most cases, 3D mode may provide a direct visualization on the signal intensity in some situations. Below is an example displaying the same data in different modes. While in the 3D mode, most of the navigation controls are the same as the ones mentioned previously, there is one minor difference. You are not able to change the contrast in 3D mode, instead, holding CTRL key while scrolling the mouse wheel will change the height of the peaks.
The export button (4) is self-explanatory. Many images in this post are created this way. It supports over-sampling up to 8x, which will generate a much bigger image with smooth font for print.
The fold button (5) toggles the control panel between the full panel mode and mini panel mode. The mini panel can save you some screen space especially on old, low resolution monitors.
The synchronize button (6) will synchronize the m/z and RT position across all samples in the result. This is very useful when you are examining a peptide feature and wondering what the same area will look like in other samples. Instead of manually navigate to the same m/z and RT region in a second sample, you only need to make sure that this button is selected and then change to the sample you want to look at. PEAKS will automatically navigate to the same area with the same zoom level and contrast.
The help button (7) displays a small dialog to provide a quick help on the navigation controls.
The following example is from a PEAKS DB result with all the checkboxes selected. The pink circle represents the center of a peptide feature. The empty blue square indicates a MS/MS spectra. The solid blue square means that the MS/MS spectra has a confident peptide identification passed the score filter. The solid yellow square means that although the MS/MS spectra does not have a confident identification, it produced a de novo only tag.
Mouse over the circles and squares will display more information. Clicking on the squares will pop up the spectrum alignment view and you can examine the MS/MS spectra directly.
In the label free quantification result, you may see two type of pink circles in the heatmap view, solid and empty. They all mean that PEAKS has detected a feature there, the solid circle indicates that the feature has passed the filters. Clicking on a pink circle will highlight the approximate boundary of that feature. You can highlight multiple features by holding the CTRL key when clicking the mouse button.
If the result related to multiple samples, all the thumbnails will be listed here. You can quickly switch between samples by a simple clicking on the sample thumbnail you want to look at.
The LCMS view can be found on any opened data nodes, identification results and label free quantification results. It contains four main components: the main heatmap view, the control panel, the TIC and the thumbnails.
Heatmap View
In the heatmap, we use the color to represent the strength of the LC-MS signals. The darker the color the stronger the signal. The x-axis is the m/z and the y-axis is the retention time.Navigation control
The operations to zoom in/zoom out and move the view is very similar to Google Map. Scroll the mouse wheel forward to zoom in and scroll backward to zoom out. Drag the mouse while holding the left mouse button to move the view. In some situation, you may want to zoom only on one axis. This can be achieved by scrolling the mouse wheel while the mouse cursor is on the RT axis or the m/z axis. You can also drag the mouse holding the right mouse button to quickly zoom into that selected area if you know exactly where you want to look at.Adjust the contrast
Scrolling the mouse wheel while holding the CTRL key will adjust the contrast of the heatmap. This is particularly useful when looking at less intense area that the default contrast cannot visually distinguish the signal strength. Here is an example. The heatmap is zoomed into a very small region. The image on the left uses the contrast works better when zooming all the way out and viewing the entire heatmap. But in this local region, the colors are all the same. You cannot visually distinguish the strength of the signal. The image on the right displays the same region with the contrast adjusted.Control Panel
The control panel is on the upper right corner of the heatmap view. It provides information such as the m/z and RT of the mouse cursor location, along with many other functions associated with the heatmap.Intensity display cut-off
The slider (0) can be used to adjust the intensity cut-off. Any peaks with an intensity less than this cut-off will not be displayed. This is very useful when you want to focus on the real signal and get a much cleaner view. This slider only affect the heatmap display. We use a much sophisticate algorithm to do the noise removal in our feature detection.The Buttons
The back and forward buttons (1) provide an easy way to restore the view to a previous state. PEAKS remembers all the operations you have done to the view, including zooming, moving and changing contrast.The 1:1 button (2) will immediately zoom out in the view to display the full heatmap. You can also invoke this function by double clicking your left mouse button anywhere in the heatmap.
The 3D button (3) toggles the view between heatmap and 3D mode. While the heatmap mode is sufficient in most cases, 3D mode may provide a direct visualization on the signal intensity in some situations. Below is an example displaying the same data in different modes. While in the 3D mode, most of the navigation controls are the same as the ones mentioned previously, there is one minor difference. You are not able to change the contrast in 3D mode, instead, holding CTRL key while scrolling the mouse wheel will change the height of the peaks.
The export button (4) is self-explanatory. Many images in this post are created this way. It supports over-sampling up to 8x, which will generate a much bigger image with smooth font for print.
The fold button (5) toggles the control panel between the full panel mode and mini panel mode. The mini panel can save you some screen space especially on old, low resolution monitors.
The synchronize button (6) will synchronize the m/z and RT position across all samples in the result. This is very useful when you are examining a peptide feature and wondering what the same area will look like in other samples. Instead of manually navigate to the same m/z and RT region in a second sample, you only need to make sure that this button is selected and then change to the sample you want to look at. PEAKS will automatically navigate to the same area with the same zoom level and contrast.
The help button (7) displays a small dialog to provide a quick help on the navigation controls.
Jump to an area quickly
The text box (8) can be used to jump to a m/z and RT position quickly if know the numbers. The format is m/z white space RT (e.g. 420.83 26.25). PEAKS will center the view on the provide coordinates and determine an appropriate zoom level.Display options
In the control panel, there is a group of checkboxes (9) that controls whether or not to overlay certain information on the heatmap. Depending on the result type, it may include features, MS/MS spectra, identified peptides and de novo only tags.The following example is from a PEAKS DB result with all the checkboxes selected. The pink circle represents the center of a peptide feature. The empty blue square indicates a MS/MS spectra. The solid blue square means that the MS/MS spectra has a confident peptide identification passed the score filter. The solid yellow square means that although the MS/MS spectra does not have a confident identification, it produced a de novo only tag.
Mouse over the circles and squares will display more information. Clicking on the squares will pop up the spectrum alignment view and you can examine the MS/MS spectra directly.
In the label free quantification result, you may see two type of pink circles in the heatmap view, solid and empty. They all mean that PEAKS has detected a feature there, the solid circle indicates that the feature has passed the filters. Clicking on a pink circle will highlight the approximate boundary of that feature. You can highlight multiple features by holding the CTRL key when clicking the mouse button.
TIC
PEAKS displays the TIC beside the heatmap RT axis. You can zoom in/out on the RT axis by scroll the mouse wheel on the TIC. When zoomed in, PEAKS will highlight the chunk of RT that is being displayed in the heatmap view. You can drag the boundary of the highlighted portion to adjust the zoom level or you can drag the middle of the highlighted portion of move the heatmap content along the RT axis.Thumbnails
The thumbnails are small, un-zoomable version of the heatmaps. It provides an overall preview of the sample. The contrast is connected to the corresponding heatmap, so changes to the contrast of a heatmap also apply to the thumbnail. PEAKS displays a rectangle on the thumbnail to highlight the area current viewed in the heatmap. You can adjust the area by scrolling the mouse wheel on the thumbnail or drag the borders, effectively, it zooms in/out in the heatmap. You can also drag the middle of the rectangle to quickly move the viewing area in the heatmap.If the result related to multiple samples, all the thumbnails will be listed here. You can quickly switch between samples by a simple clicking on the sample thumbnail you want to look at.
Monday, December 2, 2013
Boost your analysis speed with PEAKS 7
New mass spectrometry instruments come out every year with higher resolution and/or scan rate. This causes an increasing amount of data generated per hour. While the accuracy and sensitivity of the software tools are critical, many researchers have the need to complete the analysis sooner without compromising the accuracy or sensitivity.
In PEAKS 7, we have re-engineered many parts of the algorithms to make them more efficient.
Test data and search parameters
12 files generated from Thermo Q-Exactive instrument was used. Both MS and MS/MS were acquired on high resolution. In total, there are more than 100,000 MS/MS spectrum.
Test hardware and operating system
Mac mini late 2012 version. Intel i7-3720QM processor at 2.6GHz. 16GB RAM. Windows 7 Professional Edition 64 bit. The Windows OS is installed using Boot Camp.
The test and the result
PEAKS 6 and PEAKS 7 were installed on the same Mac mini computer. The computer was rebooted between analysis.
First off, we want to test our much loved de novo sequencing speed improvement and here is the result. PEAKS 7 de novo is more than five time faster!
The complete analysis in PEAKS can identify database peptides, novel peptides, PTMs and mutated peptides in one go. We use the total running time in version 6 as the baseline and see how much shorter researchers can finish the same analysis.
The same search completed in just one quarter of what it takes in the previous version, with the same level of accuracy and sensitivity.
In PEAKS 7, we have re-engineered many parts of the algorithms to make them more efficient.
"The increase in speed [of PEAKS 7] is quite remarkable."In this post, we will use an internal test to illustrate the dramatic speed improvements our users love.
Paul Taylor, Sick Kids Hospital
Test data and search parameters
12 files generated from Thermo Q-Exactive instrument was used. Both MS and MS/MS were acquired on high resolution. In total, there are more than 100,000 MS/MS spectrum.
Test hardware and operating system
Mac mini late 2012 version. Intel i7-3720QM processor at 2.6GHz. 16GB RAM. Windows 7 Professional Edition 64 bit. The Windows OS is installed using Boot Camp.
The test and the result
PEAKS 6 and PEAKS 7 were installed on the same Mac mini computer. The computer was rebooted between analysis.
First off, we want to test our much loved de novo sequencing speed improvement and here is the result. PEAKS 7 de novo is more than five time faster!
The complete analysis in PEAKS can identify database peptides, novel peptides, PTMs and mutated peptides in one go. We use the total running time in version 6 as the baseline and see how much shorter researchers can finish the same analysis.
The same search completed in just one quarter of what it takes in the previous version, with the same level of accuracy and sensitivity.
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