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Mass Spectral Data
Biodesix Inc can accept mass spectral data for analysis in the following formats.
The basic format is a set of 2-column plain text (ASCII) files, each file
containing a single spectrum. The first column should contain the mass/charge
ratio (in Da), the second column – the signal, i.e. counts. Each line in the
file corresponds to a data point in the spectrum.
Columns may be space separated, like this:
499.845424 166.607
499.860707 117.605
499.875990 140.268
499.891273 150.069
499.906557 158.031
............
Columns may also be comma separated like this
3999.847045,99.239
3999.890274,142.116
3999.933505,76.5756
3999.976735,117.615
4000.019965,135.991
. . . . . . . . .
All lines starting with non-numeric characters, such as header lines, are
ignored. A typical MALDI-TOF spectrum contains from about 10000 to about 100000
data points.
In addition to 2-column plain text files, Biodesix Inc can also accept
mass spectra in Applied Biosystems Voyager (.dat) format and in the Applied
Biosystems 4700 Proteomics Analyzer (.t2d) format.
Subject information file format
The set of spectra should be accompanied by the Excel table containing
additional information on each sample, such as disease stage, etc. One of its
columns should contain the filenames for the corresponding mass spectra files.
An example of such a table describing two files is shown below:
| ID |
Filename |
Age |
Gender |
Histology |
T |
N |
M |
Stage |
Survival |
| Case1 |
C1-ad-001.txt |
74 |
M |
adenocarcinoma |
T2 |
N0 |
M0 |
Ib |
22.6 |
| Case2 |
C2-ad_001.txt |
42 |
F |
Squamous |
T2 |
N1 |
M0 |
IIb |
30.0 |
For more details and inquires about our Services: call 970.870.9041
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