What is the language of this mass spectrophotometry data processing output file
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6.6 years ago
serpalma.v ▴ 70

Dear community, I have been assigned a task to retrieve information from files that were processed from raw mass spectrophotometry data (file.mzML). These files have just ".data" as extension and when I open them, I cannot recognize the language and therefore I cannot load them into R and work on them.

The files with the .data extension are contained in this folder:

ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD000299/

Could someone take a look at any of the files and tell me the language is in (e.g. F010439)?

Thank you very much!

mass spectrophotometry output • 1.6k views
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Take a look at http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList for tools that work with Mass Spec data.
File formats for Mascot tools are described here.

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6.6 years ago

it looks like a set of files merged together with as a HTTP multipart response: https://www.w3.org/Protocols/rfc1341/7_2_Multipart.html

$ curl  -D - "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD000299/F010439.dat" | more


MIME-Version: 1.0 (Generated by Mascot version 1.0)
Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="parameters"

LICENSE=Licensed to: INRA Tours, P-F Proteomique Analytique & Fonction.,Nouzilly (0085-0000003524/1), (2 processors).
MP=
NM=
COM=
IATOL=
IA2TOL=
IASTOL=
IBTOL=
IB2TOL=
IBSTOL=
IYTOL=
IY2TOL=
IYSTOL=
SEG=
SEGT=
SEGTU=
LTOL=
TOL=5
TOLU=ppm
ITH=
ITOL=0.8
ITOLU=Da

it contains many files generated with 'mascot'

$ curl -s -D - "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD000299/F010439.dat" | grep Content-Type |  more
Content-Type: text/plain
Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="parameters"
Content-Type: application/x-Mascot; name="masses"
Content-Type: application/x-Mascot; name="unimod"
Content-Type: application/x-Mascot; name="enzyme"
Content-Type: application/x-Mascot; name="taxonomy"
Content-Type: application/x-Mascot; name="header"
Content-Type: application/x-Mascot; name="summary"
Content-Type: application/x-Mascot; name="decoy_summary"
Content-Type: application/x-Mascot; name="peptides"
Content-Type: application/x-Mascot; name="decoy_peptides"
Content-Type: application/x-Mascot; name="proteins"
Content-Type: application/x-Mascot; name="query1"
Content-Type: application/x-Mascot; name="query2"
Content-Type: application/x-Mascot; name="query3"
Content-Type: application/x-Mascot; name="query4"
Content-Type: application/x-Mascot; name="query5"
Content-Type: application/x-Mascot; name="query6"
Content-Type: application/x-Mascot; name="query7"
Content-Type: application/x-Mascot; name="query8"
Content-Type: application/x-Mascot; name="query9"
(...
Content-Type: application/x-Mascot; name="query6495"
Content-Type: application/x-Mascot; name="query6496"
Content-Type: application/x-Mascot; name="query6497"
Content-Type: application/x-Mascot; name="query6498"
Content-Type: application/x-Mascot; name="query6499"
Content-Type: application/x-Mascot; name="query6500"
Content-Type: application/x-Mascot; name="query6501"
Content-Type: application/x-Mascot; name="query6502"
Content-Type: application/x-Mascot; name="query6503"
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