You could try to convert your data to mzML instead of mzXML using ProteoWizard
- maybe this solves your problem. The fix Tomas has provided will allow you to
import your data but without the mz values in your mzXML file, you won't be
able to see any MS1 data in MZmine.
mzML is a newer format replacing the older mzXML and mzData formats:
http://www.psidev.info/mzml_1_0_0%20
Best regards,
Thomas
From: Tomas Pluskal [mailto:plus...@oist.jp]
Sent: 8. december 2014 01:32
To: Developer discussion
Cc: YS LING
Subject: Re: [Mzmine-devel] Task Error: java.lang.NumberFormatException:empty
string (null:-1)
Hi YS,
The problem is that your file contains empty <precursorMz> tags, such as this:
<precursorMz precursorIntensity="0" activationMethod="HCD"></precursorMz>
I am not sure why this happens, because I think the information about the
precursor (m/z and intensity) should be retained in your raw data.
Nevertheless, I modified the mzXML import function in MZmine to handle this
case, so you will be able to load such file into future MZmine versions (2.13
or later).
Best regards,
Tomas
On Dec 5, 2014, at 19:28, YS LING
<ling8...@gmail.com<mailto:ling8...@gmail.com>> wrote:
Dear Mzmine developer,
I encountered the problem as above. I acquired the data using Agilent QqQ with
the mode Precursor Ion scan. I convert the data into mzXML but MZmine 2.12 gave
me the task error as above. Could you please give me some advice on it?
The data is quite huge and here is the link
https://www.hightail.com/download/UlRTRm80WlRWRCtGa2NUQw
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Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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