| Title: | Various Mass Spectrometry raw data example files |
|---|---|
| Description: | Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. |
| Authors: | Steffen Neumann <[email protected]>, Laurent Gatto <[email protected]> with contriutions from Johannes Rainer |
| Maintainer: | Steffen Neumann <[email protected]>, Laurent Gatto <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.52.0 |
| Built: | 2026-10-10 11:02:13 UTC |
| Source: | https://github.com/bioc/msdata |
The CE-MS test files consist of two files,
i.e. "CEMS_10ppm.mzML" and "CEMS_25ppm.mzML".
The data contains CE-MS runs of a standard mixture that contains e.g.
Lysine (at 10 ppm and 25 ppm, respectively) and the neutral EOF marker
Paracetamol (50 ppm).
The data was acquired on a 7100 capillary electrophoresis system from
Agilent Technologies, coupled to an Agilent 6560 IM-QToF-MS.
CE Separation was performed using a 80 cm fused silica capillary with an
internal diameter of 50 µm and external diameter of 365 µm.
The Background Electrolyte was 10 % acetic acid and separation was
performed at +30 kV and a constant pressure of 50 mbar.
MS detection was performed in positive ionization mode.
The raw data were then converted to an open-source ".mzML" format
(Proteowizzard) and load into R via the MSnBase::readMSData() function.
In order to reduce data size, the test data was subsequently cutted in
migration time and mz range using filterRt(rt = c(400, 900))
and filterMz(mz = c(147.1, 152.0)) from MSnBase
Liesa Salzer
x object containing a subset of LC/MS raw data from a Thermo Finnigan LCQ Deca XP
The data is a subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3,
intensity threshhold 100.000. It was collected in positive ionization mode.
xs object containing a subset of FTICR data from a Bruker APex
III FTICR. The data is a subset from 400-450 m/z, collected in positive ionization mode.
data(xs)data(xs)
The format is:
xs
The corresponding raw mzML files are located in the fticr-mzML and iontrap
subdirectory of this package.
## The directory with the mzML LC/MS files data(xs) mzMLpath <- file.path(find.package("msdata"), "iontrap") mzMLpath files <- list.files(mzMLpath, recursive = TRUE, full.names = TRUE) files if (require(xcms)) { ## xcmsSet Summary show(xs) ## Access raw data file x <- xcmsRaw(files[1]) x }## The directory with the mzML LC/MS files data(xs) mzMLpath <- file.path(find.package("msdata"), "iontrap") mzMLpath files <- list.files(mzMLpath, recursive = TRUE, full.names = TRUE) files if (require(xcms)) { ## xcmsSet Summary show(xs) ## Access raw data file x <- xcmsRaw(files[1]) x }
msdata
This function returns proteomics mass spectrometry files. These files
are all stored in the proteomics directory in the msdata
package. Each file/data is described in more details below.
proteomics(...)proteomics(...)
... |
Additional arguments passed to |
A character with file names.
Laurent Gatto <[email protected]>
For more access to mass spectrometry-based proteomics data, see the
rpx and MsDataHub packages.
The mzML files in the sciex directory in the msdata
package represent profile-mode LC-MS data of pooled human serum
samples (the same pool being measured). The samples were analyzed by
ultra high-performance liquid chromatography (UHPLC; Agilent 1290)
coupled to a Q-TOF mass spectrometer (TripleTOF 5600+ AB Sciex). The
chromatographic separation was based in hydrophilic interaction liquid
chromatography (HILIC) and performed using an Waters Acquity BEH
Amide, 100 x 2.1 mm column.
The mass specctrometer was operated in full scan mode in the mass range from 50 to 1000 m/z and with an accumulation time of 250 ms. The files represent a subset of spectra/scans from m/z 105 to 134 and from retention time 0 to 260 seconds. The files were generated in the same LC-MS run, but from different injections. Details on the individual files are provided below.
20171016_POOL_POS_1_105-134.mzML profile-mode LC-MS data of pooled human serum samples. Injection index: 1.
20171016_POOL_POS_3_105-134.mzML profile-mode LC-MS data of pooled human serum samples. Injection index: 19.
Sigurdur Smarason, Giuseppe Paglia and Johannes Rainer
## List the files in the sciex folder dir(system.file("sciex", package = "msdata"))## List the files in the sciex folder dir(system.file("sciex", package = "msdata"))