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Statistical calibration of the SEQUEST XCorr function.

ABSTRACT: Obtaining accurate peptide identifications from shotgun proteomics liquid chromatography tandem mass spectrometry (LC-MS/MS) experiments requires a score function that consistently ranks correct peptide-spectrum matches (PSMs) above incorrect matches. We have observed that, for the Sequest score function Xcorr, the inability to discriminate between correct and incorrect PSMs is due in part to spectrum-specific properties of the score distribution. In other words, some spectra score well regardless of which peptides they are scored against, and other spectra score well because they are scored against a large number of peptides. We describe a protocol for calibrating PSM score functions, and we demonstrate its application to Xcorr and the preliminary Sequest score function Sp. The protocol accounts for spectrum- and peptide-specific effects by calculating p values for each spectrum individually, using only that spectrum's score distribution. We demonstrate that these calculated p values are uniform under a null distribution and therefore accurately measure significance. These p values can be used to estimate the false discovery rate, therefore, eliminating the need for an extra search against a decoy database. In addition, we show that the pvalues are better calibrated than their underlying scores; consequently, when ranking top-scoring PSMs from multiple spectra, p values are better at discriminating between correct and incorrect PSMs. The calibration protocol is generally applicable to any PSM score function for which an appopriate parametric family can be identified.

SUBMITTER: Klammer AA

PROVIDER: S-EPMC2807930 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Statistical calibration of the SEQUEST XCorr function.

Klammer Aaron A AA Park Christopher Y CY Noble William Stafford WS

Journal of proteome research 20090401 4

Obtaining accurate peptide identifications from shotgun proteomics liquid chromatography tandem mass spectrometry (LC-MS/MS) experiments requires a score function that consistently ranks correct peptide-spectrum matches (PSMs) above incorrect matches. We have observed that, for the Sequest score function Xcorr, the inability to discriminate between correct and incorrect PSMs is due in part to spectrum-specific properties of the score distribution. In other words, some spectra score well regardle ...[more]

PMID: 19275164

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Project description:Background Improved methods for sampling outdoor-biting mosquitoes are urgently needed to improve surveillance of vector-borne diseases. Such tools could potentially replace the human landing catch (HLC), which, despite being the most direct option for measuring human exposures, raises significant ethical and logistical concerns. Several alternatives are under development, but detailed evaluation still requires common frameworks for calibration relative to HLC. The aim of this study was to develop and validate a statistical framework for predicting human-biting rates from different exposure-free alternatives. Methods We obtained mosquito abundance data (Anopheles arabiensis, Anopheles funestus and Culex spp.) from a year-long Tanzanian study comparing six outdoor traps [Suna Trap (SUN), BG Sentinel (BGS), M-Trap (MTR), M-Trap + CDC (MTRC), Ifakara Tent Trap-C (ITT-C) and Mosquito Magnet-X Trap (MMX)] and HLC. Generalised linear models were developed within a Bayesian framework to investigate associations between the traps and HLC, taking intra- and inter-specific density dependence into account. The best model was used to create a calibration tool for predicting HLC-equivalents. Results For An. arabiensis, SUN catches had the strongest correlation with HLC (R2 = 19.4), followed by BGS (R2 = 17.2) and MTRC (R2 = 13.1) catches. The least correlated catch was MMX (R2 = 2.5). For An. funestus, BGS had the strongest correlation with the HLC (R2 = 53.4), followed by MTRC (R2 = 37.4) and MTR (R2 = 37.4). For Culex mosquitoes, the traps most highly correlated with the HLC were MTR (R2 = 45.4) and MTRC (R2 = 44.2). Density dependence, both between and within species, influenced the performance of only BGS traps. An interactive Shiny App calibration tool was developed for this and similar applications. Conclusion We successfully developed a calibration tool to assess the performance of different traps for assessing outdoor-biting risk, and established a valuable framework for estimating human exposures based on the trap catches. The performance of candidate traps varied between mosquito taxa; thus, there was no single optimum. Although all the traps tested underestimated the HLC-derived exposures, it was possible to mathematically define their representativeness of the true biting risk, with or without density dependence. The results of this study emphasise the need to aim for a consistent and representative sampling approach, as opposed to simply seeking traps that catch the most mosquitoes. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05403-7.

Project description:Low-cost air pollution monitors are increasingly being deployed to enrich knowledge about ambient air-pollution at high spatial and temporal resolutions. However, unlike regulatory-grade (FEM or FRM) instruments, universal quality standards for low-cost sensors are yet to be established and their data quality varies widely. This mandates thorough evaluation and calibration before any responsible use of such data. This study presents evaluation and field-calibration of the PM2.5 data from a network of low-cost monitors currently operating in Baltimore, MD, which has only one regulatory PM2.5 monitoring site within city limits. Co-location analysis at this regulatory site in Oldtown, Baltimore revealed high variability and significant overestimation of PM2.5 levels by the raw data from these monitors. Universal laboratory corrections reduced the bias in the data, but only partially mitigated the high variability. Eight months of field co-location data at Oldtown were used to develop a gain-offset calibration model, recast as a multiple linear regression. The statistical model offered substantial improvement in prediction quality over the raw or lab-corrected data. The results were robust to the choice of the low-cost monitor used for field-calibration, as well as to different seasonal choices of training period. The raw, lab-corrected and statistically-calibrated data were evaluated for a period of two months following the training period. The statistical model had the highest agreement with the reference data, producing a 24-hour average root-mean-square-error (RMSE) of around 2 μg m -3. To assess transferability of the calibration equations to other monitors in the network, a cross-site evaluation was conducted at a second co-location site in suburban Essex, MD. The statistically calibrated data once again produced the lowest RMSE. The calibrated PM2.5 readings from the monitors in the low-cost network provided insights into the intra-urban spatiotemporal variations of PM2.5 in Baltimore.

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Statistical calibration of the SEQUEST XCorr function.

Publications

Statistical calibration of the SEQUEST XCorr function.

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