Methodology article
NITPICK: peak identification for mass spectrometry data
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* Corresponding author: Fred A Hamprecht fred.hamprecht@iwr.uni-heidelberg.de
- † Equal contributors
1 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
2 Department of Pathology, Children’s Hospital Boston, Boston, MA, USA
3 Department of Pathology, Harvard Medical School and Children’s Hospital Boston, Boston, MA, USA
4 Department of Neurobiology, Harvard Medical School and Department of Neurology, Children’s Hospital Boston, Boston, MA, USA
BMC Bioinformatics 2008, 9:355 doi:10.1186/1471-2105-9-355
Published: 28 August 2008Additional files
Additional file 1:
A zip folder containing all simulation files (R data files).
Format: ZIP Size: 11.8MB Download file
Additional file 2:
The zipped original LC/MS .wiff-file on which MarkerView was run (as acquired by the AB/Sciex QStar instrument)
Format: ZIP Size: 1.8MB Download file
Additional file 3:
The original spectrum of BSA-sample.wiff integrated over retention time (23.817-29.278 minutes) on which NITPICK was run.
Format: TXT Size: 570KB Download file
Additional file 4:
A zip-folder containing all pepex results on the simulated data.
Format: ZIP Size: 15.6MB Download file
Additional file 5:
A zip-folder containing all NITPICK results on the simulated data sets and for each SNR (SNR in 5, 10, 25, 50, 100) a R data file called
• resultList_0_’SNR’_0.1.RDA gives the peaks found by NITPICK for all spectra of a certain SNR
• lengthResultList_0_’SNR’_0.1.RDA gives the number of peaks found by NITPICK for each spectrum
• correct_0_’SNR’_0.1.RDA gives the number of correctly identified peaks found by NITPICK for each spectrum
• tooMany_0_’SNR’_0.1.RDA gives the number of incorrectly identified peaks found by NITPICK for each spectrum
• pp_resultList_0_3_0_’SNR’_0.1.RDA gives the peaks found by NITPICK for all spectra of a certain SNR after postprocessing with g=3
• lengthResultList_0_3_0_’SNR’_0.1.RDA gives the number of peaks found by NITPICK for each spectrum after postprocessing with g=3
• correct_0_3_0_’SNR’_0.1.RDA gives the number of correctly identified peaks found by NITPICK for each spectrum after postprocessing with g=3
• tooMany_0 3_0_’SNR’_0.1.RDA gives the number of incorrectly identified peaks found by NITPICK for each spectrum after postprocessing with g=3
Format: ZIP Size: 1.3MB Download file
Additional file 6:
Excel sheet containing the peaks detected by NITPICK (mz-position, charge, intensity) as well as their manual validation.
Format: XLS Size: 50KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 7:
Excel sheet containing the peaks detected by MarkerView (mz-position, charge, if available) as well as their manual validation.
Format: XLS Size: 109KB Download file
This file can be viewed with: Microsoft Excel Viewer