Both Topspin and NMRPipe can process the in-phase(IP) anti-phase (AP)-typed spectra. Here are the steps for two software.

In Topspin, for the 15N-HSQC IPAP experiment (ie. hsqcf3gpiaphsiwg):

• simply type “split ipap2” to process the FID
• Topspin will ask the process folder number (i.e. 10015, 10016)
• Go to each folder and adjust phases.

For Topspin, it added and substrated the phase and antiphase spectra, so the two generated spectra are processed representing “IP-AP” and “IP+AP”, respectively. The overlaid “IP+AP” and “IP-AP” spectra in Topspin looks like the example below:

Unfortunately, I only have a Ubuntu Linux box to process the data which can’t run Topspin. So I used NMRPipe to process the data and the procedures are shown below. In summary, we used “COADD” function to generate the IP and AP-phased FIDs, then used NMRpipe to Fourier transform both spectra. After the peak phases are corrected, use “addNMR” function to generate “IP-AP” and “IP+AP” spectra.

Step 1: Convert Bruker FID to NMRpipe FID, and COADD the IP/AP FIDs

#!/bin/csh

bruk2pipe -verb -in ./ser \
  -bad 0.0 -ext -aswap -AMX -decim 3040 -dspfvs 20 -grpdly 68 -ws 8 -noi2f  \
  -xN              2048  -yN               400  \
  -xT              1024  -yT               200  \
  -xMODE            DQD  -yMODE       States-TPPI  \
  -xSW         6578.947  -ySW         2432.708  \
  -xOBS         600.133  -yOBS          60.818  \
  -xCAR           4.699  -yCAR         116.000  \
  -xLAB              HN  -yLAB             15N  \
  -ndim               2  -aq2D         Complex  \
| nmrPipe -fn MULT -c 8.33333e+01 \
 -out ./test.fid -ov

nmrPipe -in test.fid -verb \
| nmrPipe -fn COADD -cList 1 1 -time -axis Y  \ 
# list for "1 1"
| nmrPipe -out A.fid -verb -ov

nmrPipe -in test.fid -verb \
| nmrPipe -fn COADD -cList 1 -1 -time -axis Y  \
# list for "1 -1"
| nmrPipe -out B.fid -verb -ov

Step 2: process each FID (A.fid, B.fid) like regular HSQC

#!/bin/csh

#
# Basic 2D Phase-Sensitive Processing:
#   Cosine-Bells are used in both dimensions.
#   Use of "ZF -auto" doubles size, then rounds to power of 2.
#   Use of "FT -auto" chooses correct Transform mode.
#   Imaginaries are deleted with "-di" in each dimension.
#   Phase corrections should be inserted by hand.

nmrPipe -in A.fid \
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 28.0 -p1 36.0 -di -verb         \
| nmrPipe -fn EXT -x1 12ppm -xn 5.5ppm -sw                 \
| nmrPipe -fn POLY -auto                                       \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
| nmrPipe  -fn LP -auto \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 1 -p1 0.00 -di -verb         \
| nmrPipe -fn POLY -auto                                       \
   -ov -out test-A.ft2

nmrPipe -in B.fid \
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 -37.0 -p1 36.0 -di -verb         \
| nmrPipe -fn EXT -x1 12ppm -xn 5.5ppm -sw                 \
| nmrPipe -fn POLY -auto                                       \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
| nmrPipe  -fn LP -auto \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 91 -p1 0.00 -di -verb         \
| nmrPipe -fn POLY -auto                                       \
   -ov -out test-B.ft2

Once the two spectra (test-A.ft2, test-B.ft2) are correct, we can use addNMR function in NMRPipe to generate addition and subtracted spectra.

The A and B spectra are in-phase (both duplets are in the same phase) and anti-phase. They should look like the two images below (IP on top, and AP at the bottom):

Then we can (1) "add IP and AP" and (2) "subtract IP to AP" to obtain the two separate upfield and downfield spectra.

addNMR -in1 test-A.ft2 -in2 test-B.ft2 -out testIP.ft2 -c1 1.0 -c2 1.25 -add
addNMR -in1 test-A.ft2 -in2 test-B.ft2 -out testAP.ft2 -c1 1.0 -c2 1.25 -sub

We then can use NMRpipe’s “view2D” function to take a look at the result

view2D.tcl -in1 testAP.ft2 -in2 testIP.ft2 -nlev 0