. 2023 Jul 17;20(1):103–111. doi: 10.1002/alz.13368

TABLE 1.

Determination of in vivo TDP‐43 cleavage sites in FTLD‐TDP via the identification of semi‐tryptic/semi‐chymotryptic peptides

				Human protease cleavage site ^b		HRMS data
TDP‐43 residues	Confidence level	C or N term ^a	TDP‐43 specific peptide	Predicted	Empirical	ISF ruled out ^c	MW gel fraction (kDa)	Maximal predicted MW (kDa) ^d	Appropriate MW (kDa) ^e	IDs ^f	Disease type
28–42	Low	C	✓	✓	х	nd	<28	41–163	х	2	TDP‐A/C
30–42	Low	C	✓	х	х	nd	38–55	41–163	✓	1	Unaffected
31–42	Low	C	✓	✓	х	nd	38–55	41–163	✓	1	TDP‐C
254–263	Low	C	✓	✓	х	х	<28	16–18	na	na	TDP‐B
266–276	Low	C	✓	х	х	nd	38–55	15–17	х	5	TDP‐A/B/C, tau, AD
280–293	High	C	✓	✓	✓ ²³	✓	<28	13–15	✓	7	TDP‐A/B/C
294–316	Low	N	✓	✓	х	nd	38–55	35–157	✓	2	TDP‐B
304–313	Low	C	✓	✓	х	✓	38–55	11–12	х	1	TDP‐C
341–360	Low	C	✓	✓	х	nd	38–55	10–11	х	1	TDP‐C

^{^a}

In vivo cleavage site (i.e., non‐tryptic/chymotryptic site) on the N‐ or C‐terminus of the peptide.

^{^b}

Predicted or empirical evidence of human enzymatic cleavage site based on Expasy data and previously published experiments, respectively.

^{^c}

In source fragmentation (ISF) ruled out (✓) or in (x) using retention time differences and relative alterations in hydrophobicity.

^{^d}

Molecular weight of the protein sequence based on the in vivo truncation site is consistent with the gel electrophoresis band region from which the peptide was found, including consideration of other additive potential post‐translational modifications (e.g., phosphorylation).

^{^e}

Peptide maximal molecular weight (without—with maximal predicted PTMs) and including empirical evidence.

^{^f}

Number of times the peptide was identified in both pooled and individual experiments.