Re: [spctools-discuss] SpectraST iRT normalization fail

The protein filter in the spectrast command looks a bit suspicious. The unquoted spaces might causing an issue. Could you try something like: -cf'Protein!~XXX_' Ben On Wed, Oct 28, 2015 at 6:28 AM, Eric Deutsch wrote: > I don’t recognize n[-15], but maybe if you referred to this

[spctools-discuss] amztpp user for ssh

g the right user to access the server. Thanks, Ben -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com.

[spctools-discuss] Tandem parameters format for PTM search

sure whether I should be setting the value of as well. Should I be using this to set the -80 and -98 values for neutral loss? Does anyone have a good example of what a tandem.params.xml file looks like when including common modifications in the search? Many thanks, Ben -- You receiv

Re: [spctools-discuss] Original validating protein dataset from Keller et al 2002 still available?

Many thanks! On Thursday, 11 April 2013 15:26:19 UTC-7, David Shteynberg wrote: > > The data can still be found here > https://regis-web.systemsbiology.net/PublicDatasets/omics_dataset/ > On Apr 11, 2013 3:08 PM, "Ben Temperton" > > wrote: > >> Hi th

[spctools-discuss] Original validating protein dataset from Keller et al 2002 still available?

e know where I can access the raw MS/MS data? Many thanks, Ben Temperton Oregon State University -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to

Re: [spctools-discuss] Making a subset of spectra from an mzXML file in Python

#x27;t find the spectra. Any ideas how I can regenerate the index once the poor-quality spectra have been removed? On Thursday, 14 June 2012 10:10:14 UTC-7, Jimmy Eng wrote: > > Ben, > > Have you done anything special to handle the scan numbers (which > presumably are not con

[spctools-discuss] Making a subset of spectra from an mzXML file in Python

on-parsed version) works fine. I can't get the mzXMLValidator to work on our systems (see post here https://groups.google.com/d/msg/spctools-discuss/bAxu-In-ju4/z9_g3mdWSFcJ), so I was wondering if anyone else had ever encountered a similar issue and had any tips. Many thanks, Ben --

[spctools-discuss] validateXML-java v. 4.5.2 (rev 5808) throwing java.lang.StackOverflowError on command line use

String(Unknown Source) at org.apache.xerces.impl.xpath.regex.RegularExpression.matchString(Unknown Source) I'm currently running Java 1.6, using the xercesImpl.jar supplied with the GNU tarball here<http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/validateXML-java/> Any ideas? Cheers, Ben -- You

[spctools-discuss] PTMProphet score

Is there a suggested way to interpret the site probability score calculated by PTMProphet. Is 0.9 consider a reasonable score like the other Prophets, and does it map on to an FDR somehow? Many thanks for any advice, Ben -- You received this message because you are subscribed to the Google

[spctools-discuss] Best Practice: Thermo LTQ RAW data onto Mascot

It appears to me that there are at least three good ways to search LTQ RAW data on a Mascot server (somewhat specific to my resources). My question is, which is the best, or at least the most accepted. The assumption below is that once the peak list is generated, the Mascot search params are not a

RE: [spctools-discuss] spectrast consensus RTs

Great! Thanks Eric. On Feb 2, 2012 4:02 PM, "Eric Deutsch" wrote: > Hi Ben, they are average,max,min among the replicates. > > Eric > > > > -Original Message- > > From: spctools-discuss@googlegroups.com [mailto:spctools- > > disc...@googlegr

[spctools-discuss] spectrast consensus RTs

e RetentionTime. Does anybody know what these three values represent and/or how they are calculated? I can't find this described in the documentation. Many thanks for any assistance. Best, Ben -- You received this message because you are subscribed to the Google Groups "spctools-discus

Re: [spctools-discuss] myrimatch and iprophet

xinteract (at least in my hands). If you're interested in more details on the error I can provide them, but I would also be very happy to run with a little older version of Myrimatch if you have one running with TPP 4.4.1 at ISB. Many thank, Ben On Mon, Mar 14, 2011 at 3:41 PM, Matthew Cha

Re: [spctools-discuss] myrimatch and iprophet

response. Ben On Fri, Mar 11, 2011 at 1:15 PM, Ben Collins wrote: > Hi, > > I'm trying to use myrimatch as one of a number of search engines to > combine later with iprophet. It seems that later versions of myrimatch > are doing on the fly decoy database generation, because I

[spctools-discuss] myrimatch and iprophet

from different search engines using non- identical databases? Many thanks for any advice, Ben -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from t

[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs

Thanks for the reply. Can't seem to upload to the group's list, so here is a link http://dl.dropbox.com/u/11659021/subset.7z Has two files generated below. If you want, I can include any files upstream of this conversion too if that would help. - Ben On Mar 3, 11:33 am, Matthew Chamb

[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs

mgfs. - Ben On Mar 3, 10:30 am, Brian Pratt wrote: > A well constructed mzXML file would normally be somewhat smaller than > its mzML equivalent - make sure you've got peaklist compression turned > on (IIRC the msconvert default is no compression, which seems like a > Bad Thing to

[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs

onvert, so far it simply stalls out though the file appears to be about 6GB large. If anyone has any clue about this or would like an example mzML to play with, please let me know. Thanks again for all the helpful feedback, especially about the beta. On Feb 22, 5:59 pm, ben wrote: > I didn&#

[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs

l the ideas, and for the updates about msconvert. Am bugging our AB-Sciex guy about the purported standalone converter. - Ben On Feb 22, 1:55 pm, lgillet wrote: > Hi Ben, > I do not know how you look at your runs, but the PeakView software (I > use Version 1.1) that open the raw data

[spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs

version of ProteinPilot3 and install without a lic, or is Skyline a better alternative? Sorry for the remedial questions, but reading through other posts I figured it might be best to ask before I start. Thanks for any help I can get. - Ben -- You received this message because you are subscribed to

Re: [spctools-discuss] Re: Choose which database for peptide search

UniProt are now also distributing an automatically combined database including SwissProt and TrEMBL for most fully sequenced species which they refer to as 'complete proteome'. For download an more info see here: http://www.uniprot.org/faq/15 http://www.uniprot.org/news/2009/11/03/release

Re: [spctools-discuss] Re: ASAP Ratio with Mascot Search

oup/spctools-discuss/browse_thread/thread/ce9796491d4aa0e/76c9e5c00c5483e3?lnk=gst&q=dimethyl#76c9e5c00c5483e3> Cheers, Ben On Fri, Oct 22, 2010 at 10:26 PM, Jimmy Eng wrote: > Determining light or heavy peptide is simple and shouldn't be a black > box: No variable mods on the s

Re: [spctools-discuss] RefreshParser error with Myrimatch

remember that > > bug, and that code hasn't been changed since at least March 2009. > > Latest version gives: > > > > > > > > This search was configured to allow cleavage after protein N-terminal > > methionines, which unfortunately pepXML cannot represen

[spctools-discuss] RefreshParser error with Myrimatch

ntion '.pep.xml'. I'm using the windows release version (4.3.1) on Windows Vista Business 64 bit (this configuration normally works fine with TPP). Many thanks for any suggestions, Ben # Commands for session DUQCFMUJJ on Wed Aug 11 13:41:25 2010 # BEGIN COMMAND BLOCK ## BEGIN Comman

[spctools-discuss] Spectrum Mill?

Hi, I've heard from Agilent that the new version of Spectrum Mill has mzXML and pepXML support. I was curious to know whether there were any plans to support Spectrum Mill in TPP? Thanks, Ben -- You received this message because you are subscribed to the Google Groups "spctools-disc

Re: [spctools-discuss] Re: ASAPRatio quantitation of different mods on a Lys

Fantastic. Thanks David, I'll try this out. Cheers, Ben On Wed, May 5, 2010 at 5:22 PM, dctrud wrote: > Ben, > > There are two separate searches, one with light mods static, one with > heavy mods static. We use a front-end to the TPP which does all the > steps, including tr

[spctools-discuss] Re: ASAPRatio quantitation of different mods on a Lys

Hi DT, I'm trying to use dimethylation labelled samples with TPP but I think I might not be specifying the modifications correctly. Is there any chance that you could post the relevant sections from your search params file (preferably X!Tandem if you're using this)? Many thanks, Ben

[spctools-discuss] Re: peak pick MS2

Hi Matt, Msconvert looks to be producing .mzXML 2.0 by default. This is causing an issue for the downstream software (Progenesis LC-MS). Does msconvert support any later versions of .mzXML? Thanks, Ben On Sep 30, 4:46 pm, Ben Collins wrote: > Hi Moshe, > > I'm currently using Pr

[spctools-discuss] Re: peak pick MS2

Hi Moshe, I'm currently using Progenesis LC-MS, a commercial label free analysis software. The feature finding takes a long time. I have also been able to analyse some of this data with msInspect. Cheers, Ben On Fri, Sep 25, 2009 at 7:34 AM, Moshe Olshansky wrote: > > Hi Ben, >

[spctools-discuss] Re: peak pick MS2

Hi Matt, Thanks, this seems to have done the trick. I now have a 14 GB mzXML file instead of 50 GB. I am interested to know whether the peak picking is being done with MassHunter or Proteowizard in this case? Many thanks, Ben. On Thu, Sep 24, 2009 at 2:21 PM, Matt Chambers < matthew.ch

[spctools-discuss] peak pick MS2

o AMT/label free analysis. Thanks, Ben --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from t

[spctools-discuss] Re: Xtandem from command line?

Thanks for the detailed instructions Jimmy. I'll give this a shot. Regards, Ben On Sat, Apr 25, 2009 at 5:20 PM, Jimmy Eng wrote: > > Ben, > > Your best place for help with running X! Tandem from the command line is > probably the GPM's website. > > helpful

[spctools-discuss] Re: Xtandem from command line?

Okay, thanks. I guess what I wanted to get at is how do I run Xtandem from the command line. Tandem seems to only want an mzXML file, so how do I point it at the tandem.params and the fasta database? I can't find this in any of the documentation. Thanks, Ben On Fri, Apr 24, 2009 at 4:

[spctools-discuss] Xtandem from command line?

/data; tandem c:/Inetpub/wwwroot/ISB/data/ sample.tandem.params So what's generating the sample.tandem.params file, and how do I call this from the command line? Thanks, Ben --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Goo

[spctools-discuss] XP 64 bit

I am wondering if TPP will work okay on 64 bit XP? Is anybody doing this routinely? Thanks, Ben --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email t

[spctools-discuss] Re: noise threshold in .mgf

se the --absTol flag. Do I have the usage correct? Thanks, Ben C:\Program Files\trapper>trapper -v --mzXML -c --absTol 1.0 H:\090312_5ME_po ol-r001.d H:\5ME_cent\090312_5ME_pool-r001_cent1.mzXML Settings: centroid scans: 1 compress scans: 0 verbose mode: 1 skip checksu

[spctools-discuss] noise threshold in .mgf

threshold, either at the .d to .mzXML, or at the .mzXML to .mgf step? Is there a way to clean up the .mgf files directly? Thanks, Ben --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups "spctools-discuss" grou

[spctools-discuss] Re: Changing peptide/proteinprophet

a3b1da6469/80c453c4d83e8d94?lnk=gst&q=minimum+peptide+length#80c453c4d83e8d94 Try changing the minimum peptide length to 1 and rerun the analysis Ben On Mon, Feb 9, 2009 at 5:39 PM, Fabio Cerqueira wrote: > > Hi, > > I'm afraid that the most recent version of TPP (4.1) has some

[spctools-discuss] Re: Errors using TPP 4.1: command line exceeded and fail interact.pep.xml

Hi Ulrich, I changed the minimum peptide length to 1 in petunia and it works now. Thanks very much for the info. Ben On Tue, Nov 18, 2008 at 6:23 AM, Ulrich auf dem Keller < [EMAIL PROTECTED]> wrote: > Hi Ben, > I also encountered this error using the lates svn code on OS X.

[spctools-discuss] Re: Errors using TPP 4.1: command line exceeded and fail interact.pep.xml

e xinteract output is pasted below. Many thanks, Ben run_in c:/Inetpub/wwwroot/ISB/data/081117_liv_OGE_2; xinteract -Ninteract.pep.xml -p0.05 -l7 -x20 -O c:/Inetpub/wwwroot/ISB/data/081117_liv_OGE_2/081105_glob_liv_pool_OGE02.pep.xml c:/Inetpub/wwwroot/ISB/data/081117_liv_OGE_2/081105_glob_l

[spctools-discuss] Re: Errors using TPP 4.1: command line exceeded and fail interact.pep.xml

6f6c1b6642/3964bd1420c56c9d?lnk=gst&q=ionscore#3964bd1420c56c9d Brian, did you have any luck with this? I'm happy to upload some files if that would be useful. Many thanks, Ben # Commands for session PRV6Q0TAN on Mon Nov 17 12:53:05 2008 # BEGIN COMMAND BLOCK ## BEGIN Command Execution ## [

[spctools-discuss] Re: trapper problem

f data that I really want to convert and start analyzing. Many thanks, Ben On Thu, Oct 9, 2008 at 12:53 PM, Ben Collins <[EMAIL PROTECTED]> wrote: > Hi Natalie, > Just to update, I have now encountered the problem with .d from a data > dependent type acquisition collected in centroi

[spctools-discuss] Re: trapper problem

e: C:\MS\test2.mzXML total number of expected scans: 21126 single mode file Device Type: 6 Initialization complete. (got computer name: BEN-PC) .100/21126 .200/21126 .300/21126 ... .8100/21126 .8200/21126 ...ERROR at .\MHDACWrapper.cpp, 227: HR = -21

[spctools-discuss] Re: trapper problem

Hi Natalie, I've compressed and uploaded a file to your FTP server called test1.d.zip Thanks, Ben On Sat, Oct 4, 2008 at 8:08 PM, Natalie Tasman <[EMAIL PROTECTED]>wrote: > Hi Ben, > Thanks for confirming the issue on XP. If you zip the directory ("compress > folder

[spctools-discuss] Re: trapper problem

rward it on Monday. Many thanks for your help. Ben On Fri, Oct 3, 2008 at 8:13 PM, Natalie Tasman <[EMAIL PROTECTED]>wrote: > Hi Ben, > > Like all of the SPC software, we don't test on Vista (we just don't have > the machines and resources to test on), so there is some

[spctools-discuss] trapper problem

C:\Program Files\trapper>trapper --mzXML C:\msBID\ratliv\test1.d single mode file (got computer name: BEN-PC) ERROR at .\MHDACWrapper.cpp, 227: HR = -2147024882 error getting spectrum empty scan object A pretty big mzXML file is created (70MB mzXML from 20MB .d) but when I try to open it with Insilic