Aligns multiple liquid chromatography-mass spectrometry (LC-MS) datasets to one another by clustering mass and chromatographic elution features across datasets. The MultiAlign application provides advanced visualization and manipulation capabilities for LC-MS datasets acquired on high resolution mass spectrometers. Functionalities include overlaid 2D plots, alignment plots, normalizations, and basic statistical comparisons. MultiAlign uses the LCMSWARP algorithm to align LC-MS datasets to a master list (mass tag database or a single LC-MS dataset) and then consolidate features into a consensus map. These features can be matched to an accurate mass and time (AMT) tag database to identify the LC-MS features.
Allows comparison of proteomics projects. PEP-Miner is a software that grafts clustering-based applications. This tool is designed to study large-scale shotgun proteomics projects. It integrates a knowledgebase of spectra and proteins useful to identify different types of information. It can detect several types of peptides (from a lot of proteins) and has diminished over 500 000 spectra to less 21 000 clusters.
Provides an implementation of clustering and merging methods for MS/MS data. Spectrum Clustering is a user-friendly software that supports various methods for spectrum similarity scoring, clustering, and merging. This application presents a graphical user interface to the user, which is divided into sections that correspond with the different tasks that can be performed: “input”, “similarity options”, “clustering options”, “merging options”, and “output”.
Identifies monoisotopic masses of precursors for tandem mass spectrometry (MS/MS) spectra. pParse proposes a method for determining candidate clusters and classifying them according the sum of the intensity, the similarity of the experimental and the theoretical isotopic distribution, and the similarity of elution profiles. The application was developed to be utilized with Thermo FT/Orbitrap RAW files.
An open-source Java library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce and Apache Spark frameworks for cluster computing was implemented.
Allows tandem mass spectra (MS/MS) clustering. msCRUSH is based on the locality sensitive hashing (LSH) technique and on an iterative clustering strategy. It serves to make similarity comparison between tandem mass spectra. This tool needs to group all spectra from the same peptides into the same clusters. It is useful for clinical proteomic datasets and other molecules such as metabolites from metabolomics.