Question

Split mzID file with mzID() function

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Brem • 0

@b78be34e

Last seen 3.3 years ago

Spain

Hi everyone, I am trying to split a mzID file that contains information from 24 mgf files (the info about my file is posted below). My intention is to create 3 independent mzID files using mzID package, one file with the info from the first 8 mgf files, another for the next 8 ngf files and the last one with the last 8 mgf files. Is it possible, has it sense?

The option of create the 3 mzID files directly from the origin (in my case from PEAKS software) is not valid for me since I have no access to the full version of the software.

Thank you for your help, Alex

This is the information about my data, read it with mzID()

#loading data
> EE2 <- "peptides_1_1_0.mzid"
#mzID 
> mzEE2 <- mzID(EE2)
reading peptides_1_1_0.mzid...
> files(mzEE2)
$id
[1] "peptides_1_1_0.mzid"

$raw
                                                                                                                    location
1  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135709.mgf
2  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135710.mgf
3  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135711.mgf
4  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135712.mgf
5  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135713.mgf
6  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135714.mgf
7  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135715.mgf
8  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135716.mgf
9  file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135801.mgf
10 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135802.mgf
11 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135803.mgf
12 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135804.mgf
13 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135805.mgf
14 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135806.mgf
15 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135807.mgf
16 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135808.mgf
17 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135809.mgf
18 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135810.mgf
19 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135811.mgf
20 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135812.mgf
21 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135813.mgf
22 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135814.mgf
23 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135815.mgf
24 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135816.mgf
               id                           IDFormat
1   SPECTRADATA_1 multiple peak list nativeID format
2   SPECTRADATA_2 multiple peak list nativeID format
3   SPECTRADATA_3 multiple peak list nativeID format
4   SPECTRADATA_4 multiple peak list nativeID format
5   SPECTRADATA_5 multiple peak list nativeID format
6   SPECTRADATA_6 multiple peak list nativeID format
7   SPECTRADATA_7 multiple peak list nativeID format
8   SPECTRADATA_8 multiple peak list nativeID format
9   SPECTRADATA_9 multiple peak list nativeID format
10 SPECTRADATA_10 multiple peak list nativeID format
11 SPECTRADATA_11 multiple peak list nativeID format
12 SPECTRADATA_12 multiple peak list nativeID format
13 SPECTRADATA_13 multiple peak list nativeID format
14 SPECTRADATA_14 multiple peak list nativeID format
15 SPECTRADATA_15 multiple peak list nativeID format
16 SPECTRADATA_16 multiple peak list nativeID format
17 SPECTRADATA_17 multiple peak list nativeID format
18 SPECTRADATA_18 multiple peak list nativeID format
19 SPECTRADATA_19 multiple peak list nativeID format
20 SPECTRADATA_20 multiple peak list nativeID format
21 SPECTRADATA_21 multiple peak list nativeID format
22 SPECTRADATA_22 multiple peak list nativeID format
23 SPECTRADATA_23 multiple peak list nativeID format
24 SPECTRADATA_24 multiple peak list nativeID format

$database
  numDatabaseSequences
1                31997
                                                                                                location
1 file:/C:/Users/USUARIO/Documents/ProteinDatabases_nov19/Cyprinodon%20variegatus_UniProt_Proteome.fasta
                id                                name   fileFormat
1 SEARCHDATABASE_1 Cyprinodon variegatus_UniProt_sep19 FASTA format

> mzEE2
An mzID object

Software used:   PEAKS Studio (version: 10.5 (2020-02-19))

Rawfiles:        file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135709.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135710.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135711.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135712.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135713.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135714.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135715.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135716.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135801.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135802.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135803.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135804.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135805.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135806.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135807.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135808.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135809.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135810.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135811.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135812.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135813.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135814.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135815.mgf
                 file:/C:/Users/alexa/PeaksExports/Liver_maleAdults_C.%20variegatus_ALEXNov19_EXp3_PEAKS_31_export_MGF/APDAPD340135816.mgf

Database:        file:/C:/Users/USUARIO/Documents/ProteinDatabases_nov19/Cyprinodon%20variegatus_UniProt_Proteome.fasta

Number of scans: 415590
Number of PSM's: 441836

mzID • 865 views

ADD COMMENT • link 3.3 years ago Brem • 0

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Entering edit mode

This does not seem like a BiocManager question. BiocManager handles the installation and loading of packages. Please reference the right package you are trying to use in order to get accurate help.