Tutorial: Temperature dependence from a series of Bruker 2D spectra in JCAMP-DX format

Introduction

• As introduced in the multi-block JCAMP-dx tutorial, JCAMP-DX formats support a wide range of instruments, including NMR spectrometers.
• Bruker, Agilent(Varian), and JOEL can export their NMR FID or Fourier transferred spectra into JCAMP-DX NMR format.
• In this tutorial, a temperature-dependent series of TROSY spectra are converted into JCAMP-DX files by Bruker Topspin and processed by TREND
  

1. Convert spectra into JCAMP-DX format

• In topsin, open the dataset to save, Run tojdx command, or choose File -> Save menu, choose Save data set in a JCAMP-DX file.
  
• Then set Type of archive file as JCAMP IDFF/DUP, which is a data compression method
• Set "Include these data types" as "RSPEC", which means only the real part spectra will be saved. (Topspin does not support saving complex part of 2D and higher dimensional data).
  
• The resulting JCAMP-DX file contains all of the spectral parameters, such as

  ##TITLE=2H, 15N phosphorylated PMM 49.2 mg/mL
  130uL Protein+ 14uL D2O+ 1.5 uL 1M DTT
  17:30 ready 298K
  ##JCAMPDX= 6.0         $$ Bruker NMR JCAMP-DX V2.0
  ##DATA TYPE= nD NMR SPECTRUM
  ##DATA CLASS= NTUPLES
  ##NUM DIM= 2
  ##ORIGIN= Bruker BioSpin GmbH
  ##OWNER= jxzr4
  $$ 1.83.2.2.2.1 TOPSPIN     Version 3.2
  $$ 2016-11-21 16:50:13.848 -0600  TIGERS\jxzr4@BCHEM-MTHOOD7
  $$ Compression mode = diff/dup
  ##.OBSERVE FREQUENCY= 800.147784601106
  ##.OBSERVE NUCLEUS= ^1H
  ##.ACQUISITION MODE= SIMULTANEOUS (DQD)
  ##.ACQUISITION SCHEME= Echo-Antiecho
  ##.AVERAGES= 32
  ##.DIGITISER RES= 22
  ##SPECTROMETER/DATA SYSTEM= spect
  ##.PULSE SEQUENCE= b_trosyetf3gpsi
  ##.SOLVENT NAME= H2O+D2O
  ##.SHIFT REFERENCE= INTERNAL, H2O+D2O, 1, 10.55175
  ##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT)
  $$ ##TITLE= Audit trail, TOPSPIN        Version 3.2
  $$ ##JCAMPDX= 5.01
  $$ ##ORIGIN= Bruker BioSpin GmbH
  $$ ##OWNER= jxzr4
  

  However, only data blocks with NTUPLE flags are spectra data points, e.g.:

  ##NTUPLES= nD NMR SPECTRUM
  ##VAR_NAME=  FREQUENCY1,    FREQUENCY2,      SPECTRUM
  ##SYMBOL=    F1,            F2,              Y
  ##.NUCLEUS=  15N,           1H
  ##VAR_TYPE=  INDEPENDENT,   INDEPENDENT,     DEPENDENT
  ##VAR_FORM=  AFFN,          AFFN,            ASDF
  ##VAR_DIM=   1024,          512,             512
  ##UNITS=     HZ,            HZ,              ARBITRARY UNITS
  ##FACTOR=    2.85073081136719, 7.01553520114943, 1
  ##FIRST=     11026.7633587518, 3584.93848778736, 59843
  ##LAST=      8110.46573872317, 0,            114128
  ##MIN=       8110.46573872317, 0,            -28692053
  ##MAX=       11026.7633587518, 3584.93848778736, 434652230
  ##PAGE= F1=11026.76335875
  ##FIRST=     11026.7633587518, 3584.93848778736, 59843
  ##DATA TABLE= (F2++(Y..Y)), PROFILE
  511E9843K28587L71399J71595j27870B98455a39447j60615g0562C61445K88667
  501F50112o8960A49008d27817k73897K66384D080J60198o5687c7512j30016j85721
  490c53249k78022k37360J1398P3379J9158L03591E2916K79358j56003c8534F6056
  478C67966J72514o4394k25803h0426m50052m14212o5060K62894L25962a64831
  467a00860j32439j34424j45489l05759l51794J02464N29787a83818O349M831A27131
  455D77261L1295k46188A09471P3478J97798R6259k21739a51898m02660n782a64097
  443G8735i7959j11726e5991f938k71003l06782r0791L9382l3312j91345m2053
  432i02842d01148E08379O13972k01345B36027a24369A22815K25456h2299p73502
  422h55801k85067L70445c40540P9926k8334J15858o955j81836J1279d857B35563
  410I9798e8704j08244k9053c4285C88374M55663l339C80548g219A3717K03582
  399B17299Q3553A26178a34453j51309e1572D20383M24262J11290l34543A34421
  388c10673j26656J79057C6952b2934l62655k52432Q8648b68527a32151c8836A08259
  376A25876a84763l97725j21897K02392O8110l03568m69443l31490l0532K33088
  366a335828M97431c81329h3708C06830N25625L06384k22775B91428b83843o7584
  

2. Prepare X axis file (optional)

We can prepare an X axis file containing temperatures for this spectra as temp.txt:

298
300
302
304
306
308

3. Do PCA analysis on the JCAMP-DX series

• Launch trendmaingui and choose JCAMP-DX files:
  
• Press "Start" button, TREND will start working (decoding JCAMP-DX is slower than other formats, please wait patiently)
  
• When the calculation finishes, the results can be seem in the html report: