Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter.

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms; its executable files, user manual, and sample data sets are freely available at https://ms.iis.sinica.edu.tw/comics/Software_FPF.html . Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline.

Tumor-infiltrating lymphocytes contain a higher proportion of FOXP3(+) T lymphocytes in cervical cancer.

BACKGROUND/PURPOSE: The subpopulations and functions of tumor-infiltrating lymphocytes (TILs) from cervical cancer (CC) are altered. Dysfunction of TIL could be partially because of the inhibition by regulatory T (T(reg)) cells. FOXP3 is the control gene for the T(reg) cells. METHODS: We investigated the distribution of TILs and FOXP3(+) cells in CC (n = 10) and cervical intraepithelial neoplasia (n = 8) tissues. Double-immunofluorescence and confocal-based image quantitative microscopic analysis were used to calculate the number of cluster of differentiation (CD)4(+)CD25(+)FOXP3(+) T(reg) cells around the tumor cells. RESULTS: The CD4(+)CD25(+)FOXP3(+) phenotype of T(reg) cells was accumulated around the tumor cells. CC contains a significantly higher proportion of the FOXP3(+) T cells than in cervical intraepithelial neoplasia (p < 0.001). Moreover, CC with lymph node metastasis has a higher proportion of the FOXP3(+) T cells than that without lymph node metastasis (p < 0.05). CONCLUSION: The increased accumulation of T(reg) cells suggests that T(reg) cells are important in the immunopathogenesis of CC.