Sitagliptin Results in a Decrease of Truncated Apolipoprotein C1.

UNLABELLED: Apolipoprotein C1 (ApoC1) is a component of multiple lipoproteins where it performs a variety of roles in lipid metabolism and transport. ApoC1 exists as both full-length and truncated isoforms. Truncation of ApoC1 has been postulated to result from the action of dipeptidyl peptidase-4 (DPP-4), the target of a new class of diabetes drugs that includes sitagliptin phosphate. In this study, we sought to determine if oral administration of sitagliptin altered the proportion of ApoC1 isoforms circulating in humans. Results indicated a dramatic change in ApoC1 truncation, consistent with a high level of DPP-4 inhibition by sitagliptin. FUNDING: University of Minnesota, Minneapolis, MN, USA.

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies.

A functional polymorphism of apolipoprotein C1 detected by mass spectrometry.

A survey of plasma proteins in approximately 1,300 individuals by MALDI-TOF MS resulted in identification of a structural polymorphism of apolipoprotein C1 (ApoC1) that was found only in persons of American Indian or Mexican ancestry. MS/MS analysis revealed that the alteration consisted of a T45S variation. The methyl group of T45 forms part of the lipid-interacting surface of ApoC1. In agreement with an impact on lipid contact, the S45 variant was more susceptible to N-terminal truncation by dipeptidylpeptidase IV in vitro than was the T45 variant. The S45 protein also displayed greater N-terminal truncation (loss of Thr-Pro) in vivo than the T45 variant. The S45 variant also showed preferential distribution to the very-low-density lipoprotein fraction than the T45 protein. These properties indicate a functional effect of the S45 variant and support a role for residue 45 in lipid contact and lipid specificity. Further studies are needed to determine the effects of the variant and its altered N-terminal truncation on the metabolic functions of ApoC1.