http://www.matrixscience.com/
Data file
Enter the path to a data file containing mass data. Data for MS/MS ion
searches must be supplied as an ASCII file. Data for a Peptide Mass
Fingerprint can be typed or pasted into the Query window or supplied as an
ASCII file. Details of the file format can be found here. N.B. If a file name is
present in this field, any contents in the Query window are ignored.
Mascot Generic Format
The Mascot generic format for a data file submitted to Mascot is (square
brackets indicate optional elements, they should not be included in an
actual data file):
[Embedded Parameter(s)]
Query 1
[Query 2]
.
.
[Query N]
Blank lines can be used anywhere, to improve readability.
Comment lines beginning with one of the symbols #;!/ can be included
Peptide Mass Fingerprint
In the case of a Peptide Mass Fingerprint, each query is just a single peptide mass
value, with an optional second value for peak area or intensity. For example:
764.2
1231.0
1284
1944.8
2020.2
2100.35
If your MS data system outputs additional values on each line, these will be ignored.
There are two ways to change default search parameters. One way is using the search
form fields. The other is to place embedded parameters at the beginning of the data file.
For example:
COM=Digest #A6345
CLE=Lys-C
CHARGE=1+
PFA=1
764.2 2010
1231.0 2345
1284 456
1944.8 1012
2020.2 23
2100.35 566
The embedded parameters (COM, CLE, CHARGE, PFA) over-ride the entries in the
corresponding form fields, if any. All of the other search parameters default to the search
form settings.
GO Live
Peptide tolerance +/-
ppm = [observed – exact]/exact x 1e6
ppm = [100.01-100]/100 x 1e6 = 100
ppm = [500.05-500]/500 x 1e6 = 100
ppm = [1000.1-1000]/1000 x 1e6 = 100
Resolution...
...relative abundance of isotopes in nature