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A mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute Quantification (iTRAQ), have been added in this version, including a reporter ion impurity correction, a reporter ion intensity threshold filter and an option for weighted normalization to correct mixing errors. TMT/iTRAQ analysis can be performed on experiments using HCD (High Energy Collision Dissociation) only, CID (Collision Induced Dissociation)/HCD (High Energy Collision Dissociation) dual scans or HCD triple-stage mass spectrometry data. To improve measurement accuracy, we implemented weighted normalization, multiple tandem spectral approach, impurity correction and dynamic intensity threshold features.
Supports calculation of the mass and theoretical isotopic distribution of a mixture of complex biopolymers. Isotopica is a useful application for validating an observed peak alongside the theoretical one, especially one with a higher mass or a complex pattern due to the presence of more than two components or enriched stable isotopes within the isotopic distribution. It can also be used to calculate the isotopic distributions of multiple components based on the relative abundance of each component.
Provides a platform for quantifying large-scale proteomic data using stable isotope-labeling techniques. MAXIC-Q is a flexible web application processing in several stages: first, it filters data before investigating ion level. Then, it performs the validation of peptide ion and processes both peptide and protein level. It accepts various inputs such as search results from Mascot, SEQUEST and ProteinProphet software and provides visualization of the studied data that includes Elution3D, XIC and PIMS diagrams.
EMU / Elementary metabolite units
Identifies minimum amount of information needed to simulate isotopic labeling within a reaction network. EMU is a bottom-up modeling approach based on a highly efficient decomposition algorithm. The functional units generated by the decomposition algorithm form the new basis for generating system equations that describe the relationship between fluxes and isotopomer abundances. This approach is valid for any stable-isotope measurement and any labeling input.
An open-source solution for Kalman filter (KF) isotope trace (IT) detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2-alternative IT detection engines-Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy.
An efficient tool for quantification of the stable isotope labeling mass spectrometry data. SILVER implements novel methods for quality control of quantification at spectrum, peptide and protein levels respectively. Several new confidence filters and indices are applied to improve the accuracy of quantification results. Additionally, SILVER provides user-friendly interfaces for parameter setting, quantitative analysis, result visualization and manual validation as well as some useful statistics analyses.
A package for extracting and analysing isotopic patterns from liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-MS (GC-MS) data relative to labelling experiments. IsotopicLabelling estimates the isotopic abundance of the employed stable isotope (either 2H or 13C) within a specified list of analytes. IsotopicLabelling is based on the assumption of having uniform labelling, and therefore the value it returns is the average C occurrence. This package has been designed to be easy to use and it provides a number of functions to quickly look at and save the results.
ASAPRatio / Automated Statistical Analysis on Protein Ratio
Calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data. ASAPRatio utilizes the signals recorded for the different isotopic forms of peptides of identical sequence and numerical and statistical methods, such as Savitzky-Golay smoothing filters, statistics for weighted samples, and Dixon's test for outliers, to evaluate protein abundance ratios and their associated errors. It also provides a statistical assessment to distinguish proteins of significant abundance changes from a population of proteins of unchanged abundance.
Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed and accuracy of the database search. Each protein obtains a score by adding its three highest peptide CAA scores, and the protein feature of a peptide is the maximum score of the proteins containing this peptide. PEAKS also provides a user-friendly interface to show each resultant peptide spectrum match from de novo sequencing.
Allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass accuracy leading to fewer false positive peptide identifications. Algorithms to increase data quality include an MS(3) score for peptide identification and a post-translational modification (PTM) score that determines the probability that a modification such as phosphorylation is placed at a specific residue in an identified peptide. MSQuant supports relative protein quantitation based on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches.
Tackles the individual aspects of a liquid chromatography-mass spectrometry (LC-MS) experiment. LaCyTools deals with multiple charge states, giving an output per charge state if desired, and offers various analyte and spectra quality criteria. The tool is able to perform tr alignment, mass spectra calibration, targeted data integration of all isotopes of a list of user defined analytes and calculating quality criteria (QC). It is an accurate automated data processing tool for high throughput analysis of LC-MS glycoproteomics data.
MassChroQ / Mass Chromatogram Quantification
A versatile software that performs LC-MS data alignment and peptide quantification by peak area integration on extracted ion chromatograms. MassChroQ is suitable for quantification with or without labelling and is not limited to high-resolution systems. Peptides of interest (for example all the identified peptides) can be determined automatically, or manually by providing targeted m/z and retention time values. It can handle large experiments that include protein or peptide fractionation (as SDS-PAGE, 2-D LC). It is fully configurable. Every processing step is traceable, the produced data are in open standard formats and its modularity allows easy integration into proteomic pipelines. The output results are ready for use in statistical analyses.
Seven Golden Rules
Automatically excludes wrong molecular formulas. Seven Golden Rules consists in (1) applying heuristic restrictions for number of elements during formula generation, (2) performing LEWIS and SENIOR check, (3) performing isotopic pattern filter, (4) performing H/C ratio check, (5) performing NOPS ratio check, (6) performing heuristic HNOPS probability check and (7) performing -TMS check. The software can also be used to calculate and subtract over 40 usual adduct ions in LC/MS applications.
An enhanced proteomic result reporting tool for MaxQuant, which is widely used in various types of proteomic studies such as in peptide identification, modification assignment, isotope labelling quantification and label-free quantification. MaxReport can automatically optimize and organize the results of MaxQuant. MaxReport also provides additional functions including generating visualization figures and exporting integrated results for users who are not familiar with bioinformatics to save time in comprehending and interpreting the results.
A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. ICPL_ESIQuant is able to process mass spectrometric data from various vendors and implements results from the Mascot search engine to generate protein and peptide result tables. Requiring MS raw data in .mzXML file format and Mascot search results in .dat format as input, ICPL_ESIQuant reliably quantifies ICPL labeled proteins and provides additional information about all detected, sequenced and identified features in the sample. The software supports both the shotgun and the directed proteomics strategy, enabling the user to apply mass inclusion lists for identifying peptides not fragmented in the first MS cycle.
A comprehensive suite to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. With dynamic extracted ion chromatogram plots, the ability to view every MS spectra at any time point and the ability to manually select a peak area, ProteoIQ® provides the ultimate level of control. ProteoIQ® provides a completely customizable interface to support any form of biological annotation. You can easily compare protein quantitative results in relation to biological pathways, protein localization, protein function, or even compare to transcript abundance. Every protein identification in ProteoIQ® can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or even an in-house LIMS.
RAAMS / Regression Analysis Applied to Mass Spectrometry
Interprets spectra of 18O-labeled peptides without requiring chemical composition information derived from product ion spectra. RAAMS is able to measure the effective 18O incorporation rate due to variable enzyme substrate specificity of the pseudosubstrate during the isotope exchange reaction and corrects for the 18O(0) abundance that remains in the labeled sample when using a two-step digestion/labeling procedure. We have also incorporated a method for distinguishing pure 18O(0) from pure 18O(2) peptides utilizing impure H2 18O. RAAMS is fast enough (average, 38 ms/spectrum) to allow the possibility of performing information-dependent MS/MS on a chromatographic time scale on species exceeding predetermined ratio thresholds.
Provides a unified, open-source framework for protein identification and quantitation. TandTRAQ combines results from database searching and peptide quantitation for producing a table with protein identifications and associated abundance ratios for each protein based on an analysis of the peptide associated reporter ions. The software was assessed using cerebrospinal fluid (CSF) samples from a childhood Acute Lymphoblastic Leukemia (ALL) study by Children’s Oncology Group and Oregon Health and Science University.
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