Development of a synchronous motion-tracking and video capture tool for flexible ureteroscopy.

INTRODUCTION: Hand/instrument motion-tracking in surgical simulation provides valuable data to improve psychomotor skills and can serve as a formative evaluation tool. Motion analysis has been well-studied in laparoscopic surgery; however, there are essentially no studies looking at motion-tracking for flexible ureteroscopy (fURS ), a common surgical procedure requiring hand dexterity and 3D spatial awareness. We aimed to design a synchronized motion-tracking and video capture system for fURS capable of collecting objective metrics for use in surgical skills training. METHODS: Motion tracking of the ureteroscope was performed using a motion-tracking platform, inertial measurement units (IMUs), and an optical sensor. Position (x, y, z) and orientation (roll, pitch, yaw) of the ureteroscope handle, lever deflection, and translation of the scope insertion point were collected. Video capture of the operator's hands was collected with a Raspberry Pi camera. All peripherals were controlled on a Raspberry Pi 4 and synchronized to its system clock. RESULTS: Our system demonstrated good accuracy in detecting translation of the ureteroscope in the x- and y-axes, and yaw, pitch and roll of the ureteroscope at discrete orientations of 0, ±30, ±60, and ±90 degrees. Unique to fURS, deflection of the lever was captured by the difference in IMU static accelerations with good accuracy. The optical sensor detected translation of the ureteroscope at the insertion point with good precision and an average error of 5.51%. CONCLUSIONS: We successfully developed a motion-tracking and video-capture system capable of collecting motion-analysis parameters unique to fURS . Future studies will focus on establishing the construct validity of this tool.

An Autonomous Continuous Bladder Irrigation System.

Introduction and Objective: Continuous bladder irrigation (CBI) is used in a variety of clinical settings, including post-transurethral surgery and the emergency department. Currently, CBI administration relies on nurses to diligently monitor and switch irrigation bags, as well as titrate the inflow rate based on effluent color. Inappropriate administration can result in discomfort to patients, clot urinary retention, repeat injury to the pathologic or surgical site, extended hospital stays, and even operative management. Our objective was to create an autonomous CBI system that decreases the incidence of disrupted irrigation flow and monitors the outflow to alert clinicians of critical events. Methods: 3D printing and off-the-shelf microcontrollers were used to design a device to fit the needs identified by stakeholders at our institution. An in vitro model of the bladder was created to test our design. The mechanical, electrical, and software subsystems were adjusted accordingly to meet our design requirements. Results: Our in vitro CBI model was able to simulate routine CBI administration with sudden bleeding. Bovine blood was used to simulate the bleeding events. A device was created that met identified stakeholder needs. Accurate detection of critical bleeding events, catheter blockage, and empty irrigation bags were achieved. The device responds to bleeding appropriately by increasing the irrigation rate. When the catheter is blocked, it stops the irrigation and alerts the nurse. Our system accurately titrated the irrigation rate to match a set outflow blood level parameter, conserving irrigation and minimizing nursing workload. Continuous monitoring of CBI effluent was recorded. Conclusions: We anticipate our device will decrease the cognitive load on nurses in busy clinical settings and improve workflow. Moreover, the detection of critical events will likely decrease patient morbidity. Continuous monitoring of the CBI outflow may prove to be a new clinical decision-making tool for ongoing hematuria. Clinical trial is pending.

A Novel Ureteroscopy Training Platform That Utilizes CT Urograms to Replicate Complex Renal Collecting System Anatomies.

Introduction: Flexible ureteroscopy (fURS) is a one-person surgical technique, limiting trainees' ability to practice intraoperatively. Although well suited for simulation training, few existing fURS simulators can accurately reproduce complex renal collecting system anatomies. We developed an anatomically accurate fURS simulator using three-dimensional (3D) reconstruction of CT urograms and 3D printing technology to address this need. Materials and Methods: Patient-specific CT urograms were used to create 3D reconstruction of the renal collecting system using Slicer™. 3D models were modified using Blender™. Hollow, elastomer kidney models were created using an Objet 3D™ printer. To test and evaluate the new fURS simulator, 25 volunteers were recruited (5 novices, 13 residents, and 7 urologists). Participants were asked to explore the model with fURS and were evaluated on their ability to deduce its 3D anatomy, their ability to navigate to prespecified calices, and their time to task completion. Furthermore, participants were asked to compare the anatomical model with existing fURS benchtop models (Cook Medical™ and Limbs & Things™) on several criteria, including internal visualization, tactile feedback, and overall functional and teaching fidelity, in a survey. Results: We were able to create a fURS simulator that accurately replicates anatomically complex renal collecting systems. In exploring the model, we noted that unlike staff urologists, novices and residents often completely missed lower pole calices. A survey comparison between our simulator and comparable benchtop simulators revealed consistently better ratings of our simulator on all criteria (p < 0.05). Conclusions: We were able to create an anatomically accurate fURS simulator that provides a more realistic scoping experience. Preliminary testing revealed that trainees will benefit from this simulator, particularly with respect to learning how to navigate challenging collecting systems.

Refining How We Define Laparoscopic Expertise.

BACKGROUND: Traditional stratification of expertise in laparoscopic simulation assigns participants to novice, intermediate, or expert groups based on case numbers. We hypothesized that expert video assessment might refine this discrimination of psychomotor expertise, especially in light of new measurable parameters. MATERIALS AND METHODS: One hundred five participants performed a defined intracorporeal suturing task in the pediatric laparoscopic surgery simulator armed with force-sensing capabilities. Participants were stratified into novice, intermediate, and expert groups via three classification schemes: (1) number of complex laparoscopic cases, (2) self-declared level of expertise, and (3) average expert rating of participants' videos. Precision, time to task completion, and force analysis parameters (FAP = total, maximum and mean forces in three axes) were compared using one-way analysis of variance tests. P < .05 was considered significant. RESULTS: Participants stratified on the basis of case numbers and on the basis of self-declared level of expertise had statistically significant differences in time to task completion, but no significant difference in FAP. When participants were restratified according to expert assessment of their video performance, time to task completion as well as total and mean forces in X, Y, and Z axes allowed discrimination between novices, intermediates, and experts, thus establishing construct validity for the latter. Precision did not allow discrimination in any stratification scheme. CONCLUSION: Compared with traditional stratification, video assessment allows refined discrimination of psychomotor expertise within a simulator. Assessment of FAP may become a relevant tool for teaching and assessing laparoscopic skills.

Effectiveness of discovery learning using a mobile otoscopy simulator on knowledge acquisition and retention in medical students: a randomized controlled trial.

BACKGROUND: Portable educational technologies, like simulators, afford students the opportunity to learn independently. A key question in education, is how to pair self-regulated learning (SRL) with direct instruction. A cloud-based portable otoscopy simulator was employed to compare two curricula involving SRL. Pre-clerkship medical students used a prototype smartphone application, a 3D ear attachment and an otoscope to complete either otoscopy curriculum. METHODS: Pre-clerkship medical students were recruited and randomized to two curriculum designs. The "Discovery then Instruction" group received the simulator one week before a traditional lecture, while the "Instruction then Discovery" group received it after the lecture. To assess participants' ability to identify otoscopic pathology, we used a 100-item test at baseline, post-intervention and 2-week retention time points. Secondary outcomes included self-reported comfort, time spent using the device, and a survey on learning preferences. RESULTS: Thirty-four students completed the study. Analysis of knowledge acquisition and retention showed improvement in scores of both groups and no significant effects of group (F1,31 = 0.53, p = 0.47). An analysis of participants' self-reported comfort showed a significant group x test interaction (F1,36 = 4.61, p = 0.04), where only the discovery then instruction group's comfort improved significantly. Overall device usage was low, as the discovery then instruction group spent 21.47 ± 26.28 min, while the instruction then discovery group spent 13.84 ± 18.71 min. The discovery first group's time spent with the simulator correlated moderately with their post-test score (r = 0.42, p = 0.07). After the intervention, most participants in both groups (63-68%) stated that they would prefer the instruction then discovery sequence. CONCLUSIONS: Both curricular sequences led to improved knowledge scores with no statistically significant knowledge differences. When given minimal guidance, students engaged in discovery learning minimally. There is value in SRL in simulation education, and we plan to further improve our curricular design by considering learner behaviours identified in this study.

Refinement in the analysis of motion within low-cost laparoscopic simulators of differing size: Implications on assessing technical skills.

BACKGROUND: Simulation is becoming more important in the teaching and assessment of technical skills. The purpose of this study was to refine the use of motion analysis parameters (MAPs) to assess performance of a defined task in low-cost pediatric laparoscopic simulators of differing size. METHODS: 105 participants performed a defined intracorporeal suturing task in large and small pediatric laparoscopic simulators. Outcomes included MAPs - path length, extreme velocity events, and extreme acceleration events in all available degrees of freedom for novices, intermediates, and experts. ANOVA p <0.05 was judged significant. RESULTS: In the smaller simulator, all MAPs discriminated between expertise groups in all degrees of freedom. In the larger simulator, all but one MAP discriminated between expertise groups. Experts demonstrated the greatest variability in performance between the larger and smaller simulators. CONCLUSION: Analysis of motion in the performance of a defined intracorporeal suturing task allowed discrimination between novices, intermediates, and experts in large and small low-cost pediatric laparoscopic simulators. Further refinement in MAPs will determine their role in surgical education. LEVEL OF EVIDENCE: Not applicable.

Development of an Open-Source Laparoscopic Simulator Capable of Motion and Force Assessment: High Tech at Low Cost.

OBJECTIVE: Laparoscopic simulators help improve surgical skills in an ex vivo setting. New simulators incorporate force and motion assessment, but often at high financial cost. Our goal is to establish global access to a laparoscopic simulator, which offers both traditional summative assessment (time to task completion and precision) as well as advanced formative assessment (force and motion sensing capabilities) so that educators anywhere may be able to create simulators with increased educational value. DESIGN: A low-cost laparoscopic simulator incorporating an off-the-shelf optical sensor, inertial measurement unit, holders, and a housing unit for a microcontroller was integrated into a plastic box with a high-definition digital camera and a three-dimensional mouse. Open source software was developed to offer real-time feedback in force and motion. The system was calibrated for accuracy and consistency. RESULTS: The simulator was assembled from off-the-shelf components and open-source software. Total estimated cost was $350 United States Dollars. The mouse was calibrated by applying known forces in known directions. Linear forces measured in all axes showed linear output trends with r2-values of between 0.988 and 0.999. Accuracy in motion evaluation was evaluated and this demonstrated low average errors in the motion sensors of 5.4% to 6.8%. CONCLUSIONS: This low-cost, off-the-shelf, open-access laparoscopic simulator provides accurate and consistent measures of force and motion. We believe that collaborative efforts between surgeons and engineers can allow the creation of these surgical teaching devices at a reasonable cost such that they can be used in resource-rich and resource-limited settings.

Comparison of Adult and Pediatric Surgeons: Insight into Simulation-Based Tools That May Improve Expertise Among Experts.

BACKGROUND: Laparoscopic models are increasingly recognized as important tools in surgical training. The purpose of this study was to compare pediatric and adult laparoscopic surgical skills, and gain insight into the upskilling in both groups. MATERIALS AND METHODS: Adult- and pediatric-sized laparoscopic simulators were fitted with custom-built motion tracking hardware and software. Participants were recruited at the Education Booth of the 2012 combined SAGES/IPEG meeting. They each performed 1 adult and 1 pediatric intracorporeal suturing task. Velocity, acceleration, and range were studied in all degrees of freedom available during laparoscopic surgery (pitch, yaw, roll, and surge). Participants were stratified by expertise based on the traditional metrics of self-reported caseloads. RESULTS: A total of 57 participants (15 novices, 7 intermediates, and 35 experts) were recruited. Experts had significantly higher extreme events in three of the four degrees of freedom when using the pediatric simulator than when using the adult simulator. Few significant differences were seen when comparing novice and intermediate performances on the adult versus pediatric simulator. Linear regression showed no difference between adult and pediatric experts tested on the adult or pediatric simulator. CONCLUSIONS: Experts were more challenged with the pediatric than with the adult suturing task. No difference was noted for overall averaged performance metrics comparing adult and pediatric experts suturing in adult versus pediatric simulators. As a participant's level of expertise improves, a model progressing from larger to smaller domains in the performance of defined laparoscopic tasks may, by virtue of its greater challenge, encourage psychomotor development.

Educational Role for an Advanced Suturing Task in the Pediatric Laparoscopic Surgery Simulator.

BACKGROUND: Laparoscopic models are recognized as important training tools. Lower fidelity systems are used mainly for simpler tasks; an advanced suturing task may allow for additional training of experts. The purpose of this study was to explore the educational role of an advanced suturing task using motion analysis and establish the task's construct validity. METHODS: The pediatric laparoscopic surgery (PLS) simulator was customized with motion-tracking hardware and software. Participants were stratified by expertise, then performed an advanced task involving intracorporeal suturing in a vertical plane, with the suture passing superiorly to inferiorly. Traditional PLS scores were calculated, and motion was analyzed in the four degrees of freedom available in laparoscopic surgery (Pitch, Yaw, Roll, and Surge). Data were compared to historic results for a standard suturing task. RESULTS: Sixty participants were recruited (8 novices, 13 intermediates, and 39 experts). Analysis of motion in all degrees of freedom allowed discrimination between participants based on expertise level. Compared with the standard task, PLS scores for the advanced task were significantly lower for intermediates and experts, and the number of extreme motion events was significantly higher, indicating that advanced task is more challenging. In addition, only 76.3% of experts, 76.9% of intermediates, and 37.5% of novices were able to successfully complete the advanced task. CONCLUSIONS: Performance of an advanced intracorporeal suturing task allowed discrimination of expertise level. The task's increased complexity may help hone laparoscopic technical skills, particularly among advanced performers, and even allow discrimination of psychomotor expertise within the traditional cohort of experts.

Video assessment of laparoscopic skills by novices and experts: implications for surgical education.

BACKGROUND: Previous investigators have shown that novices are able to assess surgical skills as reliably as expert surgeons. The purpose of this study was to determine how novices and experts arrive at these graded scores when assessing laparoscopic skills and the potential implications this may have for surgical education. METHODS: Four novices and four general laparoscopic surgeons evaluated 59 videos of a suturing task using a 5-point scale. Average novice and expert evaluator scores for each video and the average number of times that scores were changed were compared. Intraclass correlation coefficients were used to determine inter-rater and test-retest reliability. Evaluators were asked to define the number of videos they needed to watch before they could confidently grade and to describe how they were able to distinguish between different levels of expertise. RESULTS: There were no significant differences in mean scores assigned by the two evaluator groups. Novices changed their scores more frequently compared to experts, but this did not reach statistical significance. There was excellent inter-rater reliability between the two groups (ICC = 0.91, CI 0.85-0.95) and good test-retest reliability (ICC > 0.83). On average, novices and experts reported that they needed to watch 13.8 ± 2.4 and 8.5 ± 2.5 videos, respectively, before they could confidently grade. Both groups also identified similar qualitative indicators (e.g., instrument control). CONCLUSION: Evaluators with varying levels of expertise can reliably grade performance of an intracorporeal suturing task. While novices were less confident in their grading, both groups were able to assign comparable scores and identify similar elements of a suturing skill as being important in terms of assessment.

Analysis of motion in laparoscopy: the deconstruction of an intra-corporeal suturing task.

BACKGROUND: This study analyzes instrument motion for segments of a defined intra-corporeal suturing task in a laparoscopic simulator. We describe a system providing real-time velocity and acceleration assessment in the performance of this task. Analysis of the deconstructed task segments allows targeted assessment and teaching. METHODS: A traditional box trainer was fitted with a custom-built motion-tracking system. Participants were stratified into novice, intermediate and expert groups. They performed a defined intra-corporeal suturing task. Real-time data were collected in four degrees of freedom (DOFs) (Roll, Surge, Pitch, Yaw). The task was then deconstructed into four segments: loading needle/pull-through, double-throw knot, first single-throw knot, and second single-throw knot. Motion analysis parameters (MAPs) were studied for each DOF. RESULTS: Sixty-four participants were tested (14 novices, 19 intermediates, 31 experts). The largest difference in MAPs was seen in the 'double-throw knot' segment. MAPs for the 'loading needle/pull-through' segment revealed differences between novices and experts in Roll and Pitch DOFs only. For the 'first single knot' segment, similar MAP trends were noted across all DOFs, with significant differences between novices versus experts and intermediates versus experts. For the 'second single knot' segment, the difference in MAPs was preserved only for novices versus experts. CONCLUSIONS: By analyzing motion for a defined suturing task in a laparoscopic simulator, we can gain insight into the specific hand motions distinguishing experts from non-experts. Such information may allow teaching in a more focused, effective and efficient manner.

Objective Evaluation of Otoscopy Skills Among Family and Community Medicine, Pediatric, and Otolaryngology Residents.

INTRODUCTION: The objective of this study is to evaluate and compare the perceived need for otolaryngology training and otoscopy diagnostic skills in primary care (Family and Community Medicine, Pediatric Medicine), and Otolaryngology Head and Neck Surgery (OTO-HNS) postgraduate trainees. Participant otoscopy skills were evaluated using the OtoSim simulator. METHODS: Family and Community Medicine, Pediatric, and OTO-HNS residents were recruited. Each resident participated in 3 separate otoscopy training and assessment sessions. The ability to correctly identify middle ear pathology was objectively evaluated using OtoSim™. Pretest, posttest, and 3-month retention test results were compared among residents in a paired comparison paradigm. Survey data assessing exposure to OTO-HNS during undergraduate and postgraduate training were also collected. RESULTS: A total of 57 residents participated in the study. All residents reported limited exposure to OTO-HNS during undergraduate medical training. Primary care trainees performed poorly on pretest assessments (30% ± 7.8%; 95% CI). Significant improvement in diagnostic accuracy was demonstrated following a single 1-hour teaching session (30%-62%; p < 0.001). Primary care residents demonstrated a significant decrease in diagnostic accuracy at a 3-month follow-up assessment (62%-52%, p < 0.001). Self-perceived comfort with otology was poorly correlated to pretest performance among primary care trainees (r = 0.26) and showed a stronger positive correlation among OTO-HNS trainees (r = 0.56). CONCLUSIONS: A single teaching session with an otoscopy simulator significantly improved diagnostic accuracy in primary care and OTO-HNS trainees. Improved performance is susceptible to deterioration at 3 months if acquired skills are not frequently used. Self-perceived comfort with otology may not be an accurate predictor of otoscopic diagnostic skill.

Evaluation of an otoscopy simulator to teach otoscopy and normative anatomy to first year medical students.

OBJECTIVE/HYPOTHESIS: Our study evaluates the effectiveness of the OtoSim as an educational tool for teaching otoscopy and normal middle ear anatomy to first-year medical students. STUDY DESIGN: Cross-sectional survey design. METHODS: A large group otoscopy simulator teaching session was held in January 2014 for 29 first-year medical students at the University of Toronto. Following the training session, survey questions were administered to assess the student experience. RESULTS: A total of 29 students completed the survey. All respondents rated the overall quality of the event as very good or excellent. Ninety-three percent of respondents indicated that the simulator increased their confidence in otoscopy. Students also commented that they were able to learn normal middle ear anatomy without causing discomfort to patients. CONCLUSIONS: The use of otoscopy simulation is a novel addition to traditional learning methods for undergraduate medical students. Students can effectively learn normal external and middle ear anatomy and improve their confidence in performing otoscopy examination. LEVEL OF EVIDENCE: NA.

Construct validity and educational role for motion analysis in a laparoscopic trainer.

BACKGROUND: Laparoscopic models for ex vivo up-skilling are becoming increasingly important components of surgical education. This study aims to establish the construct validity and possible educational role of a new laparoscopic box trainer equipped with a motion-tracking device. METHODS: A structured questionnaire was used to assign participants into novice, intermediate, or expert categories according to level of experience in minimal access surgery (MAS). Participants carried out a well-defined intracorporeal suturing task. Three specific motion analysis parameters (MAPs)-velocity, acceleration, and range-were measured and analyzed as movements in the four degrees of freedom available in traditional MAS using tracking sensors at the trocar insertion sites. RESULTS: The number of extreme velocity and acceleration events in all four degrees of freedom proved capable of differentiating between participants in the three categories of surgical experience using an ANOVA test (p < 0.001). Post hoc analysis confirmed these differences in the number of extreme velocity and acceleration events between all groups tested except for the velocity of the roll between the intermediates and experts. CONCLUSION: These findings confirm construct validity for this new laparoscopic box trainer system, which employs a novel analysis based on motion parameters. Motion parameters provide information regarding the overall smoothness of the operator's instrument handling, an important aspect of a surgeon's technique. This preliminary data will be used to design a simulator with real-time motion feedback to enhance its educational value.

Motion analysis in the pediatric laparoscopic surgery (PLS) simulator: validation and potential use in teaching and assessing surgical skills.

BACKGROUND: Construct validity for the pediatric laparoscopic surgery (PLS) simulator has been established through a scoring system based on time and precision. We describe the development and initial validation of motion analysis to teach and assess skills related to pediatric minimal access surgery (MAS). METHODS: Participants were asked to perform a standardized intracorporeal suturing task. They were classified as novices, intermediates, and experts. Motion in the four degrees of freedom available during traditional MAS (PITCH, YAW, ROLL and SURGE) was assessed using range, velocity, and acceleration. RESULTS: Analysis of motion allowed discrimination between the 75 participants according to level of expertise. The most discriminating motion parameter was the acceleration in performing the ROLL (pronation/supination) with values of 30±27 for novices, 15±5 for intermediates, and 3.7±3 for experts (p<0.001). CONCLUSIONS: Tracking and analyzing the motion of instruments within the PLS simulator allow discrimination between novices, intermediates, and experts, thus establishing construct validity. Further development may establish motion analysis as a useful "real time" modality to teach and assess MAS skills.

The Pediatric Laparoscopic Surgery (PLS) simulator: methodology and results of further validation.

BACKGROUND: The Pediatric Laparoscopic Surgery (PLS) simulator is the only validated tool for pediatric Minimal Access Surgery. Construct validity (the ability to discriminate between novice, intermediate and expert) for the PLS simulator had previously been established on the basis of the total PLS score, as well as the individual performance on three of the five tasks. We describe the process and methods used to establish independent construct validity for a fourth task: pattern-cutting. METHODS: After considering various options for the possible modifications of the task itself, we retrospectively altered the way the pattern-cutting task was scored by modifying the weighting of precision versus time without changing the task itself. This was subsequently tested prospectively at the 2011 Canadian Association of Pediatric Surgeons meeting. RESULTS: Modification in the scoring metrics allowed differentiation within a previously tested cohort of 84 candidates (20 novices: score=48 ± 16, 19 intermediates: score=59 ± 18, 45 experts: score=69 ± 12 p=0.01). This was validated prospectively in a cohort of 18 experts and 7 intermediates (65 ± 8, 54 ± 17 p=0.03). CONCLUSIONS: Construct validity for the pattern-cutting task was established by modification of the scoring metrics. This was validated both retrospectively and prospectively.

Accurate samples for testing mass spectrometry based peptide quantification algorithms.

Quantitative proteomic experiments use algorithms to estimate peptide abundances from spectra. The efficacy of these algorithms is usually tested against a contrived mixture of proteins. However, the numerous error sources in mass spectrometry based proteomics experiments must be accounted for to evaluate novel algorithms in an unbiased manner. We set out to examine how to best utilize a set of calibration data for this purpose. We demonstrated that calibration data will have substantial noise whose magnitude depends on whether comparisons are made within or across experiments. We then propose a novel method of testing algorithms that uses the natural isotopic envelope of peptides to minimize measurement noise. We show that the variability of isotopic peptide ratios is an order of magnitude lower with this approach than with typical standard protein mixtures. We conclude by demonstrating the usefulness of this new technique in the analysis of typical peak picking algorithms.

Methods for combining peptide intensities to estimate relative protein abundance.

MOTIVATION: Labeling techniques are being used increasingly to estimate relative protein abundances in quantitative proteomic studies. These techniques require the accurate measurement of correspondingly labeled peptide peak intensities to produce high-quality estimates of differential expression ratios. In mass spectrometers with counting detectors, the measurement noise varies with intensity and consequently accuracy increases with the number of ions detected. Consequently, the relative variability of peptide intensity measurements varies with intensity. This effect must be accounted for when combining information from multiple peptides to estimate relative protein abundance. RESULTS: We examined a variety of algorithms that estimate protein differential expression ratios from multiple peptide intensity measurements. Algorithms that account for the variation of measurement error with intensity were found to provide the most accurate estimates of differential abundance. A simple Sum-of-Intensities algorithm provided the best estimates of true protein ratios of all algorithms tested.

A Bayesian approach to peptide identification using accurate mass and time tags from LC-FTICR-MS proteomics experiments.

In high-throughput proteomics, one promising approach presently being explored is the Accurate Mass and Time (AMT) tag approach, in which reversed-phase liquid chromatography coupled to high accuracy mass spectrometry provide measurements of both the masses and chromatographic retention times of tryptic peptides in complex mixtures. These measurements are matched to the mass and predicted retention times of peptides in library. There are two varieties of peptides in the library: peptides whose retention time predictions are derived from previous peptide identifications and therefore are of high precision, and peptides whose retention time predictions are derived from a sequence-based model and therefore have lower precision. We present a Bayesian statistical model that provides probability estimates for the correctness of each match by separately modeling the data distributions of correct matches and incorrect matches. For matches to peptides with high-precision retention time predictions, the model distinguishes correct matches from incorrect matches with high confidence. For matches to peptides having low-precision retention time predictions, match probabilities do not approach certainty; however, even moderate probability matches may provide biologically interesting findings, motivating further investigations.

Quantification of uncertainty of peptide retention time predictions from a sequence-based model in LC-MS/MS proteomics experiments.

In high-throughput mass spectrometry-based proteomics, it is necessary to employ separations to reduce sample complexity prior to mass spectrometric peptide identification. Interest has begun to focus on using information from separations to aid in peptide identification. One of the most common separations is reversed-phase liquid chromatography, in which peptides are separated on the basis of their chromatographic retention time. We apply a sequence-based model of peptide hydrophobicity to the problem of predicting peptide retention times, first fitting the model parameters using a large set of peptide identifications and then testing its predictions using a set of completely different peptide identifications. We demonstrate that not only does the model provide reasonably accurate predictions, it also provides a quantification of the uncertainty of its predictions. The model may therefore be used to provide checks on future tentative peptide identifications, even when the peptide species in question has never been observed before.