MS²PIP: a tool for MS/MS peak intensity prediction

Motivation: Tandem mass spectrometry provides the means tomatch mass spectrometry signal observations with the chemical entities that generated them. The technology produces signal spectra that contain information about the chemical dissociation pattern of a peptide that was forced to fragment using methods like collision-induced dissociation. The ability to predict these MS 2 signals and to understand this fragmentation process is important for sensitive high-throughput proteomics research. Results: We present a new tool called (MSPIP)-P-2 for predicting the intensity of the most important fragment ion signal peaks from a peptide sequence. (MSPIP)-P-2 pre-processes a large dataset with confident peptide-to-spectrum matches to facilitate data-driven model induction using a random forest regression learning algorithm. The intensity predictions of (MSPIP)-P-2 were evaluated on several independent evaluation sets and found to correlate significantly better with the observed fragment-ion intensities as compared with the current state-of-the-art PeptideART tool

MS²PIP prediction server : compute and visualize MS² peak intensity predictions for CID and HCD fragmentation

We present an MS2 peak intensity prediction server that computes MS2 charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published (MSPIP)-P-2 model for Orbitrap-LTQ CID spectra. Predicted MS2 spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

(MSPIP)-P-2 is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the (MSPIP)-P-2 web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we have added specialized models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides, and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run (MSPIP)-P-2, and have completely rebuilt the web server, which now allows predictions of up to 100 000 peptide sequences in a single request. The MS(2)PIPweb server is freely available at https://iomics.ugent.be/ms2pip/

Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times

Accurate prediction of liquid chromatographic retention times from small-molecule structures is useful for reducing experimental measurements and for improved identification in targeted and untargeted MS. However, different experimental setups (e.g., differences in columns, gradients, solvents, or stationary phase) have given rise to a multitude of prediction models that only predict accurate retention times for a specific experimental setup. In practice this typically results in the fitting of a new predictive model for each specific type of setup, which is not only inefficient but also requires substantial prior data to be accumulated on each such setup. Here we introduce the concept of generalized calibration, which is capable of the straightforward mapping of retention time models between different experimental setups. This concept builds on the database-controlled calibration approach implemented in PredRet and fits calibration curves on predicted retention times instead of only on observed retention times. We show that this approach results in substantially higher accuracy of elution-peak prediction than is achieved by setup-specific models

A simulated annealing optimization of audio features for drum classification

Current methods for the accurate recognition of instruments within music are based on discriminative data descriptors. These are features of the music fragment that capture the characteristics of the audio and suppress details that are redundant for the problem at hand. The extraction of such features from an audio signal requires the user to set certain parameters. We propose a method for optimizing the parameters for a particular task on the basis of the Simulated Annealing algorithm and Support Vector Machine classification. We show that using an optimized set of audio features improves the recognition accuracy of drum sounds in music fragments

Collecting ground truth annotations for drum detection in polyphonic music

In order to train and test algorithms that can automatically detect drum events in polyphonic music, ground truth data is needed. This paper describes a setup used for gathering manual annotations for 49 real-world music fragments containing different drum event types. Apart from the drum events, the beat was also annotated. The annotators were experienced drummers or percussionists. This paper is primarily aimed towards other drum detection researchers, but might also be of interest to others dealing with automatic music analysis, manual annotation and data gathering. Its purpose is threefold: providing annotation data for algorithm training and evaluation, describing a practical way of setting up a drum annotation task, and reporting issues that came up during the annotation sessions while at the same time providing some thoughts on important points that could be taken into account when setting up similar tasks in the future