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Data preprocessing software tools | MS-based untargeted proteomics

Liquid chromatography-mass spectrometry is widely used for comparative replicate sample analysis in proteomics, lipidomics and metabolomics. Before statistical comparison, registration must be established to match corresponding analytes from run to run. Alignment, the most…

Data preprocessing steps

IsotopicLabelli…
Desktop

IsotopicLabelling

A package for extracting and analysing isotopic patterns from liquid…

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.…

MSpC
Desktop

MSpC Morpheus Spectral Counter

Calculates normalized spectral abundance factor (NSAF) values from output…

Calculates normalized spectral abundance factor (NSAF) values from output obtained from Morpheus, a peptide-mass spectrometry (MS)/MS matching engine compatible with high-resolution accurate-mass…

OBI-Warp
Desktop

OBI-Warp Ordered Bijective Interpolated Warping

Aligns matrices along a single axis using Dynamic Time Warping (DTW) and a…

Aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.

Phosphonormaliz…
Desktop

Phosphonormalizer

Provides pairwise normalization of phosphoproteomics data. Phosphonormalizer…

Provides pairwise normalization of phosphoproteomics data. Phosphonormalizer allows analysis of large-scale experiments in various treatment conditions. It incorporates non-enriched data as a…

TurboRaw2MGF
Desktop

TurboRaw2MGF

There are a lot of high frequency, high abundance isobaric related ions in…

There are a lot of high frequency, high abundance isobaric related ions in MS/MS spectrum, and combining removing isobaric related ions with deisotoping and deconvolution in MS/MS preprocessing…

GPTime
Desktop

GPTime Gaussian Process Time

Predicts chromatographic retention time with gaussian processes. GPTime is a…

Predicts chromatographic retention time with gaussian processes. GPTime is a kernel based Bayesian framework that can learn a non-linear mapping between input and target values. GPTimes has provided…

MS-REDUCE
Desktop

MS-REDUCE

An algorithm for ultrafast reduction of MS/MS data in pre-processing stage. The…

An algorithm for ultrafast reduction of MS/MS data in pre-processing stage. The proposed algorithm is a low-complexity procedure based on random sampling, approximate classification and quantization…

JS-MS
Desktop

JS-MS JavaScript Mass Spectrometry

Allows visualization of specialised tree dimensional mass spectrometry (MS).…

Allows visualization of specialised tree dimensional mass spectrometry (MS). JS-MS runs as a web application without the need for any external dependencies. It is able to display mass-to-charge…

PE-MMR
Desktop

PE-MMR Post-Experiment Monoisotopic Mass Refinement

Creates a MGF file with refined parent ion masses and charges. PE-MMR can lead…

Creates a MGF file with refined parent ion masses and charges. PE-MMR can lead to more accurate search results from Mass Spectrometry (MS)/MS spectra. It is an integrated approach that combines three…

MS-Deconv
Desktop

MS-Deconv

A combinatorial algorithm for spectral deconvolution. MS-Deconv (i) generates a…

A combinatorial algorithm for spectral deconvolution. MS-Deconv (i) generates a large set of candidate envelopes, (ii) constructs an envelope graph encoding all envelopes and relationships between…

SuperQuant
Desktop

SuperQuant SuperQuant node

A quantitative proteomics data processing approach that uses complementary…

A quantitative proteomics data processing approach that uses complementary fragment ions to identify multiple coisolated peptides in tandem mass spectra allowing for their quantification. This…

MzJava
Desktop

MzJava

An open-source Java library for the analysis of mass spectrometry data from…

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…

Normalyzer
Desktop
Web

Normalyzer

Normalizes the uploaded data using twelve different well known normalization…

Normalizes the uploaded data using twelve different well known normalization methods and compares the resulting data based on quantitative and qualitative parameters. Normalyzer is completely…

EigenMS
Desktop

EigenMS

Uses singular value decomposition to capture and remove biases from liquid…

Uses singular value decomposition to capture and remove biases from liquid chromatography-mass spectrometry (LC-MS) peak intensity measurements. EigenMS is an adaptation of the surrogate variable…

MS-Cluster
Desktop

MS-Cluster

An efficient clustering approach for analyzing large MS/MS data sets with a…

An efficient clustering approach for analyzing large MS/MS data sets with a capability to reduce the number of spectra submitted to further analysis by an order of magnitude.

Maltcms
Desktop
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