What file format is it?
0
0
Entering edit mode
3.6 years ago
fred.s.kremer ▴ 100

I have received a few MS spectrometry results in an "ASCII" format, but have no idea in what format it is, what programs can i use to process it or how to convert it to the MGF format (which i use with X!Tandem). Here follows the first lines of one of them.

0.0196833,+,ESI,ms1,-,line,300.0000-3000.0000,12,301.1385 516,305.0270 236,352.3463 228,357.0801 252,417.0365 516,419.0414 336,421.0508 516,430.9134 532,442.8959 232,446.8765 252,525.8584 244,922.0070 232
0.0364167,+,ESI,ms1,-,line,300.0000-3000.0000,13,315.1649 256,416.0446 232,419.0431 952,420.0465 344,421.0434 632,430.9120 456,446.9005 284,481.4050 212,560.8703 268,702.8613 224,718.8335 232,922.0106 388,2121.9276 216
0.0531167,+,ESI,ms1,-,line,300.0000-3000.0000,9,301.1385 372,352.3379 216,357.0890 264,416.0305 248,417.0397 364,419.0414 596,421.0547 296,430.9135 588,446.8824 232
0.0698,+,ESI,ms1,-,line,300.0000-2999.9999,12,301.1392 604,302.1462 504,329.3161 256,347.9600 288,417.0340 324,419.0451 348,421.0475 432,430.9120 516,446.8929 244,566.8927 280,622.0387 244,1110.7699 224
0.0865,+,ESI,ms1,-,line,300.0000-2999.9999,9,301.1409 608,317.1008 268,380.2449 244,417.0368 608,419.0374 292,420.0474 220,421.0460 588,430.9143 696,446.8923 524
0.103183,+,ESI,ms1,-,line,300.0000-3000.0001,8,301.1388 408,352.3394 208,419.0443 544,421.0449 604,430.9137 368,446.8916 296,582.8623 248,990.8132 236
0.119883,+,ESI,ms1,-,line,300.0000-3000.0001,14,301.1349 400,357.0924 376,416.0407 208,417.0463 620,419.0410 728,420.0468 344,421.0444 388,422.0436 236,430.9191 344,446.8857 584,481.4146 228,495.9266 248,566.8876 252,838.8301 244
0.136583,+,ESI,ms1,-,line,300.0000-3000.0001,10,301.1445 688,357.0797 344,417.0427 520,419.0373 616,421.0394 768,422.0493 224,430.9176 392,446.8865 356,582.8588 268,838.8378 328
proteomics sequencing sequence mass spectrometry • 1.0k views
ADD COMMENT
1
Entering edit mode

I have received

Did you try asking the people you received it from?

ADD REPLY
0
Entering edit mode

Yes, but they don't know the equipment that was used, nor the protocol for data analysis. As it will take some time to get the information from the person that did the procedure, i prefer to try to discover the format based on the structure (as the analysis requires a certain urgency).

ADD REPLY
1
Entering edit mode

a certain urgency

Well, good luck. Open forums are not always great for deadline-bound problems but maybe you'll get lucky :-)

ADD REPLY
0
Entering edit mode

Have fun with that...

What is your file extention ?

ESI -> electrospray ionisation mass spectrometry (ESI-MS) ?

ADD REPLY
0
Entering edit mode

The file extension is ".ASCII" lol

ADD REPLY
0
Entering edit mode

You can try to feed msconvert with your input and see if you got in output

ADD REPLY
0
Entering edit mode

Result from mscovert:

  processing file: ascii/hboonkc.ascii
    [ReaderFail]  don't know how to read ascii/hboonkc.ascii
    Error processing file ascii/hboonkc.ascii

(╯°□°)╯︵ ┻━┻

ADD REPLY
0
Entering edit mode

Last try just change .ascii to .txt

ADD REPLY
0
Entering edit mode

Which MS product gives you these outputs ? Do you have an header line or something ?

ADD REPLY
0
Entering edit mode

No header, only lines of data.

ADD REPLY
0
Entering edit mode

Same thing, but thanks all of you for the help, i will wait the response of the technician that did the analysis.

processing file: ascii/hboonkc.txt
[ReaderFail]  don't know how to read ascii/hboonkc.txt
Error processing file ascii/hboonkc.txt
ADD REPLY
0
Entering edit mode

Someone ask the same thing here to convert to mzXML : Converting text format Mass spectrometry data to mzXML?

ADD REPLY

Login before adding your answer.

Traffic: 1578 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6