Hi

There is a good example of a study using Mahalanobis distance 

Rodriguez-Saona LE, Khambaty FM, Fry FS, Dubois J, Calvey EM. Detection and

identification of bacteria in a juice matrix with Fourier transform-near infrared

spectroscopy and multivariiate analysis. J Food Prot. 2004 Nov;67(11):2555-9.

PubMed PMID: 15553641.

but most groups  use Euclidean distance 

Cebi N, Yilmaz MT, Sagdic O. A rapid ATR-FTIR spectroscopic method for

detection of sibutramine adulteration in tea and coffee based on hierarchical

cluster and principal component analyses. Food Chem. 2017 Aug 15;229:517-526.

doi: 10.1016/j.foodchem.2017.02.072. Epub 2017 Feb 22. PubMed PMID: 28372210.

Zhang J, Huang P, Wang Z, Dong H. Application of FTIR spectroscopy for

traumatic axonal injury: a possible tool for estimating injury interval. Biosci

Rep. 2017 Jul 21;37(4). pii: BSR20170720. doi: 10.1042/BSR20170720. Print 2017

Aug 31. PubMed PMID: 28659494; PubMed Central PMCID: PMC5567294.

or squared Euclidean distance

Fuenffinger N, Arzhantsev S, Gryniewicz-Ruzicka C. Classification of

Ciprofloxacin Tablets Using Near-Infrared Spectroscopy and Chemometric Modeling.

Appl Spectrosc. 2017 Aug;71(8):1927-1937. doi: 10.1177/0003702817699624. Epub

2017 Apr 10. PubMed PMID: 28393531.

For general multivariate analysis of NIR data the following is quite helpful but doesn't address the distance matrix directly

Rosas JG, Blanco M, González JM, Alcalá M. Quality by design approach of a

pharmaceutical gel manufacturing process, part 2: near infrared monitoring of

composition and physical parameters. J Pharm Sci. 2011 Oct;100(10):4442-51. doi:

10.1002/jps.22607. Epub 2011 May 5. PubMed PMID: 21557224.

 best wishes,

Elaine

Thank you very much Elaine!!!

Both (Mahalanobis and Euclidian) have shown good results. I suggest you try both.