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. Author manuscript; available in PMC: 2020 Jul 24.
Published in final edited form as: J Proteome Res. 2016 Aug 23;15(9):2891–2899. doi: 10.1021/acs.jproteome.5b00996

Figure 1.

Figure 1.

Mascot is significantly more accurate when screening a, b, and y ions. In assessment of conformance to parent proteins before trypsin digestion,12 all 4560 peptides detected by Mascot screening for a, b, and y CID ions were also detected when screening for only b and y ions. However, the 264 additional peptides detected only in the b/y screen had very poor conformance to parent protein MWs (62.9%; arrow). Bootstrap analysis with 2000 samples of 264 peptides (with replacement) from the a/b/y screen revealed 99% confidence limits between 79.5 and 90.9% (broken arrows). This confirms that the poor b/y conformance of 62.9% is significantly lower than the a/b/y conformance.