Testing an alternative search algorithm for compound identification with the 'Wiley Registry of Tandem Mass Spectral Data. MSforID'

Oberacher, Herbert; Graeme, Whitley; Berger, Bernd; Weinmann, Wolfgang (2013). Testing an alternative search algorithm for compound identification with the 'Wiley Registry of Tandem Mass Spectral Data. MSforID'. Journal of Mass Spectronomy, 48(4), pp. 497-504. Wiley 10.1002/jms.3185

[img] Text
testing.pdf - Published Version
Restricted to registered users only
Available under License Publisher holds Copyright.

Download (636kB) | Request a copy

A tandem mass spectral database system consists of a library of reference spectra and a search program. State-of-the-art search programs show a high tolerance for variability in compound-specific fragmentation patterns produced by collision-induced decomposition and enable sensitive and specific 'identity
search'. In this communication, performance characteristics of two search
algorithms combined with the 'Wiley Registry of Tandem Mass Spectral Data,
MSforID' (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were
evaluated. The search algorithms tested were the MSMS search algorithm
implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30,000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their Setup from tandem-in-space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Service Sector > Institute of Legal Medicine > Forensic Chemistry and Toxicology

UniBE Contributor:

Weinmann, Wolfgang


500 Science > 540 Chemistry








Katrin Renfer

Date Deposited:

24 Apr 2014 15:04

Last Modified:

11 Nov 2015 09:08

Publisher DOI:


PubMed ID:






Actions (login required)

Edit item Edit item
Provide Feedback