Processing TPPI 2D data
TPPI (Time Proportional Phase Incrementation) is one method for accomplishing phase-sensitive "quadrature detection" in the indirect dimension, most often used in Bruker experiments. The only "trick" to processing is that a real FT is required in the indirect dimension.
This should not be confused with States-TPPI data, which must be processed differently.
A recommended reference is T.D.W.Claridge, "High-Resolution NMR Techniques in Organic Chemistry", 1999.
Customization of the macros may be desirable to use different window functions or to incorporate a spectrum reverse (SR) if needed.
- Arrayed Mode (NUTS-Pro users only)
- Commands for processing 2D data
- 2D Processing details
- Processing States-TPPI data
- Processing hypercomplex data
- Processing echo-antiecho data
- Processing magnitude hetcor or COSY 2D data
- Displaying 2D data
Using Arrayed Mode, processing can be done using a macro (below) or simply by entering the following commands using the command line. NUTS-Pro users with NUTS versions newer than Nov 2002 can process data using the modified arrayed mode, such that both dimensions can be phased after processing. See below.
Users with the standard 2D version cannot use Arrayed Mode, and can process with a different macro (below).
Arrayed Mode processing from the command line
|IM||import file called ser|
|AR||enter arrayed mode|
|S#||set phase shift for sine multiplication to 90|
|MS MS||apply cosine squared window function|
|PH||phase while viewing the first slice; on exiting phase routine, the entire data set is phased|
|ZF||zero-fill (may be repeated if needed)|
|RT||Performs a real FT. This is critical!
may require phasing; see 2D phasing
|TD||to view data with direct dimension horizontal|
|MH||set minimum height to 0.3 (good starting guess for contour threshold)|
Be sure to save the processed data.
NUTS-Pro users with copies newer than Nov 2002 can process using the modified arrayed mode, allowing phasing in both dimensions after processing. Processing is as above, except that instead of the AR command, execute the following command (in non-2-letter command mode):
This creates the required additional 2 quadrants of data, filled with zeroes, and enters the pairwise arrayed mode. See details.
With NUTS versions dated May 2002 to Nov 2002, you must enter the pairwise arrayed mode before re-opening the processed data, so that the data is sorted correctly when opened. Versions newer than Nov 2002 will read the PT parameter and automatically start the pairwise arrayed mode when the file is opened.
NUTSMacro TPPI 2D for NUTS Professional ; process and phase on 1st slice before starting macro ask filea ga ; turn on arrayed mode set array_on ;window fcn is cosine squared, applied with ms ms set s# 90 process 1st dimension, phase with previously determined values bc ms ms ft ps ; transpose data td ; 2nd dimension processing with cosine sq, zero-fill and real FT ms ms zf rt bc ; set scale, set contour threshold (MH = .3) and display intensity plot ss set mh .3 ip end
This macro ends displaying data with the indirect dimension on the horizontal axis. This is because usually some phasing is needed. See 2D phasing. Note that the processed data has not been saved.
Before running the macro, import the data with IM. The macro start by prompting for a data file to open – select the translated NUTS file, which always starts with $.
Processing is done one 1 slice at a time, so the sequence of commands is done in a Link, which is repeated for each slice.
Before running the macro, import the data, FT and phase. When the macro starts, it will ask for a file to open – select the translated file. Temporary files are written at each stage of processing, so the macro must reset the file names at each stage. Be sure to save the final result.
|NUTSMacro phase-sensitive TPPI
set SL 1
set FileC ft1.2d
|The macro prompts the user for the name of the data file to be read, designated File A. Temporary file names are used for intermediate stages of processing. The file after the first dimension FT is called ft1.2d.|
|set S# 90
ga ms ms ft ps sc in
|The window function used here is cosine squared, accomplished with MS MS after setting the phase for sine multiplication to 90 degrees.
The processing Link applies the window function, FT and phases with phase parameters determined on the first slice, before the macro was started. The FT’d data is saved as File C.
|set FileA ft1.2d
set FileC td.2d
set SL 1
|The file created in the previous step becomes the input for the next step.
File C, which will be the output of the next step, is defined as td.2d.
|td||Transpose the data to access slices in the second dimension.|
| set fileA td.2d
set fileC ft2.2d
set SL 1
|The input data for the next processing step is td.2d
The slice pointer is set to slice 1 and the file opened. The file to be created in the next step is ft2.2d.
|Set S# 90
ga ms ms zf rt sc in
|Link to process in 2nd dimension uses cosine squared window function and one zero-fill.
A real transform (RT) is used instead of a "normal" FT. No phase correction is applied.
|set FileA ft2.2d
set SL 1
|The processed data, ft2.2d, is read in and the slice pointer set to 1.|
|SS normalizes the display scale. It looks through the entire data set to find the largest peak and sets it equal to 100%. Contour levels are defined in the nuts.ini file as mulitples of the Minimum Height (MH) which is expressed as a percent of the largest peak. So SS is needed to get the display correct.|
This macro ends with the second dimension displayed horizontally. It may be desirable to perform another TD operation to view the data from the better digitized dimension. It has not been done as part of the macro in case additional phasing is required. Phasing can be done as described here.
Forward linear prediction (LN) can be used in the second dimension processing instead of zero-filling. After the first dimension processing, determine the appropriate Linear Prediction parameters by testing on one or more slices. The most recent values for each parameter will be used when LN is used in a Link or macro. Then modify the macro for processing in the second dimension by replacing ZF with LN. Processing will require significantly more time when LN is included (For a 1K complex by 256 NOESY data set, processed on a Pentium 100, this macro takes about 20 min.)
Last updated: 3/23/05.