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Data preprocessing (targeted MS-based proteomic analysis)

Data preprocessing programs for targeted MS-based proteomic analysis.

specL
Desktop

specL

A versatile set of functions to generate assay panels from spectral libraries…

A versatile set of functions to generate assay panels from spectral libraries for use in targeted data extraction methods (SWATH/DIA) in the area of proteomics. The package provides a BiblioSpec…

MSnbase
Desktop

MSnbase

An R/Bioconductor package for the analysis of quantitative proteomics…

An R/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. MSnbase provides an exploratory data analysis framework for reproducible research,…

MRMPlus
Desktop

MRMPlus

Computes analytical measures as recommended recently by the Clinical Proteomics…

Computes analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for "Tier 2" assays - that is, non-clinical assays…

Diana
Desktop

Diana

A set of algorithms and tools intended for analysis of data independent…

A set of algorithms and tools intended for analysis of data independent acquisition mass spectrometry (DIA-MS) data, using a targeted extraction strategy. The algorithm is capable of providing…

TAPIR
Desktop

TAPIR TArgeted Proteomics Information Representation

A fast and efficient Python visualization software for chromatograms and peaks…

A fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats…

MassyTools
Desktop

MassyTools

A data processing tool for targeted high-throughput MALDI-MS data extraction.…

A data processing tool for targeted high-throughput MALDI-MS data extraction. MassyTools is capable of calibrating spectra, extracting data, and performing quality control calculations based on a…

Ariadne
Web

Ariadne

A method to correlate tandem mass spectra of sample RNA nucleolytic fragments…

A method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based…

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…

Swiss Mass…
Web
Desktop

Swiss Mass Abacus

Calculates peptide and glycopeptide masses. Swiss Mass Abacus is purposefully…

Calculates peptide and glycopeptide masses. Swiss Mass Abacus is purposefully kept as simple as a basic calculator executing arithmetic operations. It applies a calculator using algebraic precedence…

iSRM
Desktop

iSRM Intelligent SRM

Increased quantitative throughput and selectivity for triple quadrupole mass…

Increased quantitative throughput and selectivity for triple quadrupole mass spectrometer-based assays.

Scheduled MRM
Desktop

Scheduled MRM

MRM transitions of the targeted analytes are monitored only around the expected…

MRM transitions of the targeted analytes are monitored only around the expected retention time.

tMRM
Desktop

tMRM Triggered MRM

An analytical method which is available for all Agilent Triple Quadrupole LC/MS…

An analytical method which is available for all Agilent Triple Quadrupole LC/MS systems.

mzQuantML
Desktop

mzQuantML

Improves the capabilities for open-source software development in proteomics,…

Improves the capabilities for open-source software development in proteomics, including re-analysis and visualization of data sets. Importantly, mzQuantML ensures that data sets submitted to public…

ALL-P
Desktop

ALL-P

A statistical framework based on a hierarchical modeling that takes into…

A statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances.

SRMBuilder
Desktop

SRMBuilder

Facilitates processing of the post-acquisition data files and validation of…

Facilitates processing of the post-acquisition data files and validation of quantification result for scale selected reaction monitoring (SRM). SRMBuilder analyzes large SRM data from multiple file…

iRT-Calculator
Desktop

iRT-Calculator

Convert your retention times into iRT - or iRT into retention times - on your…

Convert your retention times into iRT - or iRT into retention times - on your chromatographic set-up.

TAPAS
Web
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