ReadW and Orbitrap Exactive output files
Andris
This week I converted a number of Orbitrap Exactive files
using the installed Xcalibur (Thermo Exactive 1.1) and the current
ReadW (4.3.1).
The resulting *.mzXML files had the msLevel="0", polarity="any". Also
raw files contain scans from four different functions ESI+ full lock,
ESI+ full MZ, ESI- full lock and ESI- full MZ. All scans from these
functions are merged in one mzXML file. Is it possible to split them
in separate files or at least set correct values for "msLevel" and
"polarity"?
I can use a "filterLine" values for these task, but it requires extra
coding and hassle.
filterLine="FTMS {1;1} + p ESI Full lock ms [60.00-1200.00]"
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/
mzXML_3.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/
mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd"
>
<msRun scanCount="5214" startTime="PT0.10327S" endTime="PT2761.43S" >
<parentFile fileName="649_MeOH_A_1sliced.raw" fileType="RAWData"
fileSha1="ae4d528dc6142883f92eb0bbd5f5506cce01b904" />
<msInstrument>
<msManufacturer category="msManufacturer" value="Thermo Finnigan" /
>
<msModel category="msModel" value="unknown" />
<msIonisation category="msIonisation" value="NSI" />
<msMassAnalyzer category="msMassAnalyzer" value="FTMS" />
<msDetector category="msDetector" value="unknown" />
<software type="acquisition" name="Xcalibur"
version="1.1-133400/1.1.0.1335" />
</msInstrument>
<dataProcessing>
<software type="conversion" name="ReAdW" version="4.3.1(build Sep
9 2009 12:30:29)" />
</dataProcessing>
<scan num="1"
msLevel="0"
peaksCount="0"
polarity="any"
scanType="unknown"
filterLine="FTMS {1;1} + p ESI Full lock ms [60.00-1200.00]"
retentionTime="PT0.10327S"
lowMz="0"
highMz="0"
basePeakMz="205.159"
basePeakIntensity="94589.4"
totIonCurrent="513978" >
<peaks precision="32"
byteOrder="network"
contentType="m/z-int"
compressionType="none"
compressedLen="0" >AAAAAAAAAAA=</peaks>
</scan>
If somebody wants to investigate that,
I can upload a raw file.
Best regards,
Andris
Dominik Schwudke
not sure if it is of help for your problem but:
the Software RecalOfline from Thermo (should be part of FT-programs)
allows to split raw files according to the scan filter.
It is even mention that one should be able to run that program over
command line what never worked in my hands...(Thermo never takes such
bug reports serious anyway - and does something about it).
If your data-set is not to huge you might split up the *.raw and
convert them separately.
best
Dominik
Matt Chambers
ReAdW gets the ms level and polarity from the filter line, but in this
case it doesn't know how to deal with the filter line so it seems to be
silently aborting the filter parser. The "extra coding and hassle"
should happen to the parser code instead of your own code (IMO). But in
this case, I'm not even sure what the elements of the scan filter mean.
What is {1;1}? What is "lock" vs. "MZ"? Is that like Waters's lock mass?
-Matt
Andris Jankevics
As I understand data have 4 scanfilters: 1) negative with lockmass, 2)
negative raw, 3) positive with lockmass, and 4) positive raw.
Functions 1 and 3 are corrected to lockmass signal (no like in
Water's, just lock scans ), and 2,4 raw data.
{1;1} refers to the first scan method defined in the experiment
(positive mode in this example), and {1;2} is the second scan method
(ie negative mode in this case).
filterLine="FTMS {1;1} + p ESI Full ms [60.00-1200.00]"
filterLine="FTMS {1;2} - p ESI Full ms [60.00-1200.00]" - negative
polarity, profile mode, electrospray ionisation, raw ms (not corrected
for lockmasses).
I just checked out FilterLine.cpp code, and actually I was not able to
figure out where exactly problem can occur, but I am not a software
coder.
Dominik, yes we tried to use RecalOfline, but also in this case
"msLevel" and "polarity" are set wrong.
Thank you and best regards,
--
Andris Jankevics
AIO
Groningen Bioinformatics Centre
Groningen Biomolecular Sciences and Biotechnology Institute
University of Groningen
Kerklaan 30, Haren, 9751 NN, The Netherlands
Matthew Chambers
y refers to the scan event, what does the x refer to? Method segment?
If you need a server to upload it to:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F
Also, SPC tools team, how do I access that server? :P
-Matt
Andris Jankevics
http://bars.rug.nl/download/26c8814e3cb2770d
In this example {x;y}, x is not changing, it is always 1. But y is 1
or 2, and depends on polarity.
Thanks and best regards,
Andris
Matthew Chambers
had to use a Windows VM to view it. It indeed appears they've put scan
segment and scan event in the filter line, and have added a new keyword
("lock"). The lock keyword appears to only be applied if at least one of
the configured lock masses was found in the spectrum, in which case some
adjustment has been applied; otherwise, it won't have the lock keyword
and no adjustment is applied. It shouldn't be difficult to add support
for these changes, although I'm curious what you're planning to do with
this data once it's in mzXML format.
-Matt
Andris Jankevics
Thank you for your work, these data will be mostly metabolomics data
sets which will be analyzed by XCMS and several other software tools.
It would be nice to have functionality in ReAdW to extract only mzXML
file by based on scan event (for example only lock mass corrected
positive slice), but this is not so essential.
best regards,
Andris
Matthew Chambers
Overdue support for filter lines found in Exactive files has finally been added to ProteoWizard (as of r2087). Also there was a problem with parsing the
instrument model and that should also be fixed.
Thanks for your reports and for uploading the files.
-Matt
On 6/24/2010 3:46 PM, Zhenyu Chang wrote:
However, I have encountered the following problem when using msconvert tool. I was trying to convert a .RAW data generated by Thermo Fisher Exactive instrument
to mzML 1.1 data format.
Matthew Chambers
I don't know what a "lockmass function" is in the context of a Thermo instrument. Do you have it set
up as a separate scan event? I thought lockmass was calibrated based on finding the given masses
inside normal MS1 scans. Msconvert will certainly export ALL scan events by default, so if XCMS
isn't picking some of them up that's not an msconvert bug. :) If you WANT to export just certain
scan events, use the scanEvent filter:
# skip scan event 5
--filter "scanEvent 1-4 6-"
Hope this helps,
-Matt
On 11/1/2012 9:57 AM, Anas wrote:
> Hi all,
> How did this problem got solved eventually ? I have acquired Q-Exactive data with lockmass on (for
> metabolomics uses) and the lockmass functions seems the only one to be recognized by xcms,
> I appreciate your help,
> Cheers,
> Anas
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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>
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> proteowiza...@lists.sourceforge.net
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>
Gavin Blackburn
The "lockmass" is a separate scan filter in Thermo files that you can see in qualbrowser. If the lock mass is present throughout the experiment you get a single scan filter. When the lock mass isn't present throughout the whole experiment you get to filters, "lockmass" and "fullms". One of these scans contains all the data, and one contains just the parts relating to the specific scan header, but it seems to vary which is which. I think it is whichever if the most common throughout the experiment.
I'm pretty sure we had this problem with readw but I don't ever remember having it with msconvert, although I do remember having a conversation with someone and I've never contacted the readw people. This ring any bells with you Matt?
Anas, does the mzXML file contain all of the positive scans? If you are running pos/neg switching they'll either be all the odd or all the even numbers if you only have two scan events.
Cheers,
Gavin.
-----Original Message-----
From: Andris Jankevics [mailto:andris.j...@gmail.com]
Sent: 01 November 2012 15:17
To: Anas
Cc: proteowizard-support; Chang, Zhenyu (charlie); Matthew Chambers; spctools...@googlegroups.com
Subject: Re: [proteowizard-support] ReadW and Orbitrap Exactive output files
Hi Anas,
I believe that all measured masses are corrected on the fly during measurement (at least Waters machines does so), and stored lock-mass scans usually can be discarded by using "scanEvent" filter.
Best Regards,
Andris Jankevics
(1) Groningen Bioinformatics Center,
University of Groningen, The Netherlands
(2) Systems Biology lab, Joseph Black Building
Room B3.9, University Avenue, University of Glasgow,
Glasgow, G12 8QQ, Scotland, UK
Gavin Blackburn
Hi Anas,
The problem is a readw one, you have to specify a scan filter in readw or specify “fullms” (don’t quote me on that filter!).
MSConvert supports centroiding and I’d recommend moving to it, here is a simple batch file code:
cd C:\pwiz
msconvert C:\rprocessing\rawdata\*.raw -o C:\rprocessing\converted\posmzxmlfiles --mzXML --filter "peakPicking true 1" --filter "polarity positive" -v
cd C:\pwiz
msconvert C:\rprocessing\rawdata\*.raw -o C:\rprocessing\converted\negmzxmlfiles --mzXML --filter "peakPicking true 1" --filter "polarity negative" –v
the peak-picking filter is “peakPicking true 1”.
I can send you an rscript if you need it but it’s basically the same, I showed Stuart how to use it when he came across to see our methods so you could ask him.
Cheers,
Gavin.
From: Anas [mailto:anask...@googlemail.com]
Sent: 01 November 2012 16:00
To: spctools...@googlegroups.com
Cc: proteowizard-support; Chang, Zhenyu (charlie); andris.j...@gmail.com; Anas
Subject: Re: [proteowizard-support] ReadW and Orbitrap Exactive output files
Matt,Gavin, thanks for the quick reply,
Matt,
I meant to say lockmass filter (function in Waters terms), it is not a separate scan event, I just turned it on to improve mass accuracy, all the scans were MS1, but Thermo decided to mix the two filters together,
I am using ReAdW to convert o mzXML as I need centroid data, an option deleted by Thermo from Exactive and can`t find support for it in msconvert,
here is an example of a working (lockmass off) and a corrupted file (converted by ReAdW)
it`s certainly a Thermo bug, msconvert is not the culprit :),
Gavin,
No switching, a single polarity data,
https://icseclzt.cc.ic.ac.uk/pickup.php?claimID=YZ6QXbK3ojWU3z9D&claimPasscode=ufAeKModjUaB3ZFH&emailAddr=mkamleh%40imperial.ac.uk
Gavin Blackburn
Hi Anas,
Just looked at the files. The working one is ok because the lock mass scan filter doesn’t appear at any point in the data (as far as I can see), but the corrupted file does have this scan filter for several scans and so causes this problem.
As Matt said, MSConvert should solve the problem for you.
Cheers,
Gavin.
From: Anas [mailto:anask...@googlemail.com]
Sent: 01 November 2012 16:00
To: spctools...@googlegroups.com
Cc: proteowizard-support; Chang, Zhenyu (charlie); andris.j...@gmail.com; Anas
Subject: Re: [proteowizard-support] ReadW and Orbitrap Exactive output files
Matt,Gavin, thanks for the quick reply,
Matt,
I meant to say lockmass filter (function in Waters terms), it is not a separate scan event, I just turned it on to improve mass accuracy, all the scans were MS1, but Thermo decided to mix the two filters together,
I am using ReAdW to convert o mzXML as I need centroid data, an option deleted by Thermo from Exactive and can`t find support for it in msconvert,
here is an example of a working (lockmass off) and a corrupted file (converted by ReAdW)
it`s certainly a Thermo bug, msconvert is not the culprit :),
Gavin,
No switching, a single polarity data,
https://icseclzt.cc.ic.ac.uk/pickup.php?claimID=YZ6QXbK3ojWU3z9D&claimPasscode=ufAeKModjUaB3ZFH&emailAddr=mkamleh%40imperial.ac.uk
On Thursday, November 1, 2012 4:08:04 PM UTC+1, matt.chambers wrote:
Andris Jankevics
I believe that all measured masses are corrected on the fly during
measurement (at least Waters machines does so), and stored lock-mass
scans usually can be discarded by using "scanEvent" filter.
Best Regards,
Andris Jankevics
(1) Groningen Bioinformatics Center,
University of Groningen, The Netherlands
(2) Systems Biology lab, Joseph Black Building
Room B3.9, University Avenue, University of Glasgow,
Glasgow, G12 8QQ, Scotland, UK
On Thu, Nov 1, 2012 at 3:08 PM, Matthew Chambers
<matt.ch...@gmail.com> wrote: