MALDIquant - Quantitative Analysis of Mass Spectrometry Data

A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

Last updated 3 months ago

maldimaldi-imsmaldi-tof-msmass-spectrometry

11.58 score 62 stars 43 packages 185 scripts 5.7k downloads

cleaver - Cleavage of Polypeptide Sequences

In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Last updated 25 days ago

proteomicsbioccleavagedigestpeptides

7.58 score 12 stars 2 packages 22 scripts 410 downloads

MALDIquantForeign - Import/Export Routines for 'MALDIquant'

Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from 'MALDIquant' objects.

Last updated 10 months ago

csvexportimportmaldimass-spectrometrymsd-filesmzml

7.28 score 10 stars 3 packages 42 scripts 680 downloads

readBrukerFlexData - Reads Mass Spectrometry Data in Bruker *flex Format

Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series.

Last updated 2 months ago

bruker-daltonicsimportmaldi-tof-ms

5.37 score 12 stars 5 packages 13 scripts 815 downloads

topdownr - Investigation of Fragmentation Conditions in Top-Down Proteomics

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

Last updated 25 days ago

immunooncologyinfrastructureproteomicsmassspectrometrycoveragemass-spectrometrytopdown

5.26 score 1 stars 220 downloads

readMzXmlData - Reads Mass Spectrometry Data in mzXML Format

Functions for reading mass spectrometry data in mzXML format.

Last updated 1 years ago

4.83 score 5 stars 6 packages 15 scripts 694 downloads

zlog - Z(log) Transformation for Laboratory Measurements

Transformation of laboratory measurements into z or z(log)-value based on given or empirical reference limits as proposed in Hoffmann et al. 2017 <doi:10.1515/labmed-2016-0087>.

Last updated 2 years ago

laboratory-measurementstransformationzlog

4.00 score 2 stars 152 downloads