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Missing spectra numbers when searching MGF based spectrarecords with Tide
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Johannes  
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 More options Feb 2, 5:09 am
From: Johannes <jgri...@yahoo.com>
Date: Thu, 2 Feb 2012 02:09:40 -0800 (PST)
Local: Thurs, Feb 2 2012 5:09 am
Subject: Missing spectra numbers when searching MGF based spectrarecords with Tide
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Hi group,

I've converted several (well formatted) MGF files to spectrarecords using
the latest (modified) version of msconvert that's shipped with Tide
(1.0-x86_64-binaries). In the Tide output (sqt and text) all spectra
numbers are reported as "0". Here's an excerpt of the Tide text output:

0       1970.90 3
        0.209824        LFSLVIWICLVAMGYLFMCFGGTVSPWDQVSFFLFIIFVVYTMLPFNMR
                sp|Q08462|ADCY2_HUMAN   107     R       D
0       1971.60 3
        0.287774        LNVWVIVMIDLCTHTLGTHNTMLSVESDQFALFSLSEQTLAVHCHLCMYC
                tr|DECOY_E7ERY2|E7ERY2_HUMAN    561     R       -

Personally, I would expect to find the spectrum's index within the MGF file
as it's normally present when using Crux on MS2 files (when I converted the
MGF files to MS2 and then used Crux to search them the output was as
expected).

Thanks for any help,
Johannes


 
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