Xiaoyu Yang*, Pedatsur Neta, and Stephen E. Stein

Extending ATandem Mass Spectral Library to Include MS2Spectra ofFragment Ions ProducedIn-Source and MSnSpectra

Mass Spectrometry Data Center, National Institute of Standards and Technology

Mail Stop 8362, Gaithersburg, Maryland 20899,United States

*Corresponding author:

Additional Examples of In-Source Fragmentation.

In addition to the MS2 spectra of in-source fragment ions shown in Fig. 2b, we present below the spectra of three additional in-source ions:

Fig. S1. Examples of MS2 spectra of additional 3 in-source fragments in Fig. 2b.

Fig. S2 shows another example of the MS2 spectra of the precursor ion [M+H]+ and the in-source fragment ions [M+H-NH3]+ and [M+H-CH2O2]+ produced from β-(2-thienyl)-D-alanine. Each spectrum was recorded at various collision energies and a spectrum at one energy, which shows most of the peaks, was chosen for presentation in Fig. S2.

Fig. S2. MS2 HCD spectra of in-source fragmentation ions of β-(2-Thienyl)-D-alanine.

Clustering Spectra for the examples in Fig. 3.

In order to demonstrate how to cluster the spectra for generating the consensus spectra in Fig. 3, some examples of individual HCD MS2 spectra are shown in Fig. S3. Spectra of #1 and #2 are 2 examples of 11 spectra for generating consensus spectrum A in Fig. 3; Spectra of #3, #4 and #5 are 3 examples of 20 spectra for generating consensus spectrum B in Fig. 3. In the highlighted area, spectra #3, #4 and #5 each has a high intensity peak of 2H2O loss from the precursor (p-2H2O). However, in spectrum #1, the peak intensity of m/z 251.1432 is small and almost invisible; spectrum #2 does not have peaks in this area. So, spectra #1 and #2 are excluded from the composite spectrum. Two clusters were formed because of this 2H2O loss peak.

Fig. S3. Examples of individual HCD MS2 spectra for generating consensus spectra in Fig. 3.