Re: [spctools-discuss] PepXML > spectrum > top hits viewer issue - Comet

Sam, I believe the spectrum link reads the Comet hits from the Comet produced pep.xml file and generates the Lorikeet spectrum link from that file. Can you confirm you've corrected the mzML path in that file as well? On Mon, Feb 19, 2024 at 7:41 PM Sam Whedon wrote: > Hi all, > > I am using t

Re: [spctools-discuss] Re: EXpress in SILAC

he solution is normalization (as we do in St. Peter) >> >> so I wanted to know if such normalization is done in Express before >> calculating the light to heavy ratio. >> >> >> On Wed, Nov 22, 2023 at 3:07 PM Jimmy Eng wrote: >> >>> I don't kn

[spctools-discuss] Re: EXpress in SILAC

I don't know what "normalized intensity/peak area" of each peptide means in this context but I can say that XPRESS doesn't do any normalization. It simply reports light area to heavy area ratios. You'll have to do adjustments after the fact i.e. centering the mean ratio to 1:1 if you expect t

Re: [spctools-discuss] XPRESS peak intensity value

to get the precursor_intensity). Thank you for your help! > > On Tuesday, November 14, 2023 at 3:46:34 PM UTC-5 Jimmy Eng wrote: > >> I might need some clarification on what you're asking as XPRESS (and >> possibly the other quant tools) does extract the precursor peak

Re: [spctools-discuss] XPRESS peak intensity value

imply pull out the peak area/intensity for each peptide/precursor. On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk wrote: > Thank you! Do you know if there is any way to extract the precursor peak > intensity with XPRESS (or other TPP tools)? > > On Tuesday, November 7, 2023 at 4:32

Re: [spctools-discuss] XPRESS peak intensity value

"peak_intensity" is the maximum peak intensity of the ion chromatogram. On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk wrote: > Hello all! > I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the > "peak_intensity" output value. I was just looking to confirm whether > "peak_inte

[spctools-discuss] Re: Next proteomics informatics course?

Any plans to offer another TPP course? A user emailed me about the course so I came here to see if there was any info on a future course and saw this post w/o a reply yet. On Monday, June 12, 2023 at 9:52:33 AM UTC-7 suzmcde...@gmail.com wrote: > Hi there-is there a plan to run the proteomics i

Re: [spctools-discuss] Proteome discoverer users guide

I have a link to the 2.5 user guide that I'll send to Sanclayver directly. On Thu, May 25, 2023 at 8:35 AM Sanclayver Araújo wrote: > Hello all > Does Anyone have Proteome discoverer User Guide 2.4 and/ or 2.5? > -- > *Sanclayver Corrêa Araújo*, BPharm, MSc. > > Blogs e Podcasts: https://linktr.

Re: [spctools-discuss] protein validation

Felipe, You should not search sequence databases composed of just a single protein or even tens of proteins and hope to process them through downstream validation tools like the Prophets. When you do this, you break lots of assumptions that the tools expect which makes the results, like probabili

Re: [spctools-discuss] SILAC quantification with targeted SIM

Will, XPRESS extracts precursor intensities from MS1 scans and your mzXML file contains only MS/MS scans. So that's why XPRESS is failing because it's expecting to parse MS1 scans which aren't present in this file. Jimmy On Fri, Apr 7, 2023 at 8:57 AM Will Comstock wrote: > Hi all, > > I'm tr

[spctools-discuss] Re: Load spectra: Warning - no spectra searched : Comet

Hi. There could be a few reasons why would report a "Warning - no spectra searched" message (such as the mzML file contains only MS1 scans or the "activation_method" or "ms_level" parameters are set incorrectly). The easiest way to debug your issue is to take a look at one of your mzML files

Re: [spctools-discuss] xinteract (TPP v5.2.0) not detecting any spectra from comet output

Damian, As David noted, in Comet 2020 I unfortunately got rid of a search score that causes the behavior you're seeing. And yes, if I could go back in time, I would not have made that change again because of this noted issue. As a quick intermediate fix until you've updated to the TPP 6 release,

Re: [spctools-discuss] command "C:/TPP/bin/PeptideProphetParser" failed

Stick with Comet 2019.01.5. In version 2020.01.0, I deprecated the "deltacnstar" score in Comet and it looks like PeptideProphet can't run w/o it. Alternately, run this Perl command on your pep.xml files before running PeptideProphet if you want a workaround with the latest Comet: perl -i -pe 's

Re: [spctools-discuss] X!Tandem- Help please

Your Xeon has 6 physical cpu cores so make sure you set the number of X!Tandem threads ("spectrum, threads ") to "6" to make use of all of them as it looks like the default is "1". 6 I'd also confirm that you are intending to perform a semi-tryptic se

Re: [spctools-discuss] Comet fixed and variable modifications

Carbamidomethylation has a modification mass of 57.021464. To apply it to each peptide's n-termini if that's your intent: add_Nterm_peptide = 57.021464 This modification is commonly applied to cysteine residues: add_C_cysteine = 57.021464 For methionine oxidation as a variable modificati

Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI

help, > > Kate > > On Wednesday, 29 July 2020 13:58:44 UTC-4, Jimmy Eng wrote: >> >> Hi Kate. Your search seems to have completed fine. The "Search end:" >> text would not show up if the search terminated abruptly so I think you're >> seei

Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI

While my mzML files are in > k:/TPP/data/SpikeMix/raw > > Could that be the source for this error and can I fix it? > > Thank you for your help, > > Kate > > On Wednesday, 29 July 2020 13:58:44 UTC-4, Jimmy Eng wrote: >> >> Hi Kate. Your search seems to ha

Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI

t; Comet version "2019.01 rev. 5" > > Search start: 07/29/2020, 12:08:28 PM > - Input file: 190417_CytHumSt_1_Pep3D_Spectrum.mzML >- Load spectra: 1458 > - Search progress: 4% > - Post analysis: done > Search end:07/29/2020, 12:08:30 PM, 0m:2s > > Is

[spctools-discuss] Re: Specifying comet param file in batch file

Mark, You can specify an alternate parameters file to use using a command line option. Type the Comet binary ("comet.exe" I presume) on the command line without any input arguments to get the usage statement with the command line options. The "-P" option is to specify the parameter file e.g.

[spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command

Javan, You're not going to be able to run SEQUEST through the TPP unless you've purchased the software from Thermo and have it installed on the same computer that's running the TPP. It doesn't come with the TPP itself. And support for the SEQUEST pipeline option should probably be removed fro

[spctools-discuss] Re: Percolator Error in TPP

Confirm that you are using Comet's Percolator output which you can generate by setting "output_percolatorfile = 1" in the search parameters. This will create a tab-delimited text file with a ".pin" file extension. Note that this is different than Comet's ".txt" output file which is a different

Re: [spctools-discuss] Help in geneting Sequest and X!Tandem parameter files

s software would not work with the TPP. On Mon, Apr 13, 2020 at 12:48 PM Javan Okendo wrote: > Jimmy, > > I thought I can run it within TPP? I can see it is listed as one of the > sequence search engines within the TPP. I have not contacted the Thermo > guys yet. > > On Mon

Re: [spctools-discuss] Help in geneting Sequest and X!Tandem parameter files

Javan, Note that SEQUEST is a commercial product distributed by Thermo and does not come with the TPP. I'm not even sure if current versions of SEQUEST through Thermo are compatible with the TPP pipeline. Have you acquired SEQUEST from Thermo? On Mon, Apr 13, 2020 at 10:16 AM JAVAN OKENDO wrot

Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI

ile. You can generate > a new parameters file using "comet -p" > > > > > On Mon, Apr 13, 2020 at 7:40 PM Jimmy Eng wrote: > >> Javan, >> >> This implies the Comet search has not run. How are you attempting to >> running Comet? You mention s

Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI

Javan, This implies the Comet search has not run. How are you attempting to running Comet? You mention searchGUI in your title ... are you using the TPP to run Comet or CometOmic's SearchGUI? Jimmy On Mon, Apr 13, 2020 at 10:27 AM JAVAN OKENDO wrote: > I get the following error even though m

Re: [spctools-discuss] Interpretation of stats from pepXML viewer

Regarding inputs and output counts to Comet, as Eric mentioned, there are search parameters which affect whether or not a spectrum will be searched at all. These are: activation_method, digest_mass_range, max_precursor_charge, minimum_peaks, minimum_intensity, and remove_precursor_peak (which can

[spctools-discuss] Re: Problem installing TPP 5.2.0 in Fedora (Red Hat Enterprise Linux Server 7.6)

For your method 2 problem, see this solution posted by David back in April: https://groups.google.com/forum/#!searchin/spctools-discuss/comet$20mstoolkit%7Csort:date/spctools-discuss/6_rYJ_9aefE/D5cEw0_mBgAJ On Wednesday, August 7, 2019 at 10:11:07 AM UTC-7, sangramjit basu wrote: > > Hello, > >

Re: [spctools-discuss] RefreshParser within xinteract unable to find all proteins corresponding to identified peptides

" num_matched_ions="17" tot_num_ions="16" > calc_neutral_pep_mass="1096.5917" massdiff="0.001" num_tol_term="2" > num_missed_cleavages="0" is_rejected="0"> > > Do you know if there is a parameter similar to 'clip_nterm_me

Re: [spctools-discuss] RefreshParser within xinteract unable to find all proteins corresponding to identified peptides

Without more info, here's my educated guess at an explanation: that peptide is not a fully tryptic peptide in the proteins you list as it is preceded by a methionine residue. For isoform P06396-2, the preceding methionine is the first residue of the sequence and I'm assuming you did a Comet searc

[spctools-discuss] Re: xsl file not being created

Just to give this some closure here, Bronson not being able to open the pep.xml files was due to missing the RewriteRule directive in his webserver config. On Monday, January 7, 2019 at 10:05:13 AM UTC-8, Bronson Petterson wrote: > > I recently installed and setup TPP with the web interface. Aft

Re: [spctools-discuss] MS3 quantification

Eric, Unfortunately the Libra's MS3 TMT support is based on an optional "filterLine" attribute in the mzXML file that msconvert does not write out as far as I'm aware. Libra uses the information in the filter line to identify the ms3 scan number associated with the ms2 scan. As a workaround, you

Re: [spctools-discuss] TPP: Comet search output for decoys does not look correct (for .pep.xml and .pin files)

Francesca, Quick answer: set "decoy_search = 0" because your FASTA already has decoy entries in it. The "decoy_search" parameter controls whether or not you have Comet generate decoys "on-the-fly". Since your database already has decoy entries, you need to set "decoy_search = 0". Otherwise,

Re: [spctools-discuss] Error searching Aebersold lab's files with X!Tandem on TPP

> > Thanks! > > On Monday, October 16, 2017 at 10:53:21 PM UTC-7, Jimmy Eng wrote: >> >> How much RAM does your computer have? 158K spectra is a lot of spectra >> to load at once, especially using the k-score pluggable scoring option >> compared to native Tandem, so

Re: [spctools-discuss] Error searching Aebersold lab's files with X!Tandem on TPP

How much RAM does your computer have? 158K spectra is a lot of spectra to load at once, especially using the k-score pluggable scoring option compared to native Tandem, so there's a chance that the program ran out of memory if you don't have lots of it on your machine. Monitor task manager while

Re: [spctools-discuss] "- Search progress: Error - database file, expecting definition line here." Error with custom database

Adam, Try removing the first blank line in your fasta file and see if that fixes the problem. On Fri, Sep 29, 2017 at 8:06 AM, Adam R wrote: > Woops. Yes this is my mistake when copying/pasting into the post. But the > the fasta file attached is correct with >sp|uniprot|gene_human for all > ent

Re: [spctools-discuss] Dimethylation quantification with XPRESS (TPP 5.0)

gt; Thanks again, > Oded > > On Friday, September 22, 2017 at 7:22:39 PM UTC+3, David Shteynberg wrote: >> >> Yes this release is from code revision 7625 which includes Jimmy's patch. >> >> -David >> >> On Fri, Sep 22, 2017 at 8:07 AM, Jimmy Eng wrote: &

Re: [spctools-discuss] Dimethylation quantification with XPRESS (TPP 5.0)

is available at the > sourceforge Sashimi page? TPP_Setup_5.1.0-rc1.exe > > Best, > > Alejandro > > On Wednesday, September 6, 2017 at 10:37:10 PM UTC+2, Jimmy Eng wrote: >> >> Oded, >> >> I just checked in a fix for the issue. It will hopefully be

Re: [spctools-discuss] Dimethylation quantification with XPRESS (TPP 5.0)

Oded, I just checked in a fix for the issue. It will hopefully be available in the next TPP 5.1.0 release whenever that happens. Jimmy On Thu, Aug 31, 2017 at 7:00 AM, Oded wrote: > Hi there, > I am trying to do run a quantitative analysis of dimethylated samples > labelled on N-term and lysi

Re: [spctools-discuss] Re: TPP v5.0 in Windows 7 not generating images in Xpress nor ASAP report and protxml legacy viewer not working

Hopefully one of the other devs will chime in with a better solution. On Tue, Aug 8, 2017 at 4:09 PM, Jimmy Eng wrote: > Alejandro, > > I just had a look at this because I was going to add a long overdue minor > update to the XPRESS cgi viewer and saw that I also couldn't see th

[spctools-discuss] Re: TPP v5.0 in Windows 7 not generating images in Xpress nor ASAP report and protxml legacy viewer not working

Alejandro, I just had a look at this because I was going to add a long overdue minor update to the XPRESS cgi viewer and saw that I also couldn't see the images also on my linux install. Assuming you're building from source, edit out the following line: translate_absolute_filesystem_path_t

Re: [spctools-discuss] TPP 5.0 compilation on CentOS fails

Just to give some closure to this in case anyone else comes across this error, the solution was to remove any trailing whitespaces in the lines of the site.mk file. In this case, there was a trailing space in the first line "INSTALL_DIR = /data/bin/TPP/TPP_5.0.0 " which prompted the "mixed implici

Re: [spctools-discuss] comet component compliation fails

You should try doing google searches for the compile errors. And if you do, remove the minus sign from "-lpthread" or "-lm" because a minus sign before a term causes that term to be excluded from any search results. Another option is to quote the whole search string "/usr/bin/ld: cannot find -lm".

Re: [spctools-discuss] Comet can not perform search

This looks more like a general GUI issue rather than anything I can address in Comet. See if this resolves your problem with the TPP and different drive letters: https://groups.google.com/forum/#!topic/spctools-discuss/4cOVLmQeX60 On Fri, May 5, 2017 at 7:23 AM, 钟传奇 wrote: > Hi Jimmy, > >

Re: [spctools-discuss] TPP 5.0.0 compile error on comet.exe build: /usr/bin/ld: cannot find -lpthread

See if this page helps: http://forums.justlinux.com/showthread.php?126349-usr-bin-ld-cannot-find-lpthread I'd try editing the Makefile to remove the "-static" option first. Alternately, make sure you have libpthread.a installed. On Tue, Apr 25, 2017 at 7:17 PM, Joe wrote: > I'm using the 5.0.0

Re: [spctools-discuss] Comet search of data on D:\ [Windows 10] error

Comet defaults to "unknown" for both the instrument model and instrument manufacturer if neither of those are set in the input file. As I don't have any strong feelings about this, I just changed the code to report "UNKNOWN" which will be what's reported in the next release (which is way overdue).

Re: [spctools-discuss] Re: Libra quantification

lly just tried it again on a test file > converted to mzML and I was able to get an output for the quantitation > table, so maybe the mzXML/mzML is the difference? Is that possible? > > Best, > > chris > > > > > > > On Wednesday, October 28, 2015 at 6:49:06 P

Re: [spctools-discuss] Error while conversion of files

For a huge run, irrespective of whether it's converted in profile or centroid mode (the # of MS/MS scans is more important), be sure to set the parameter "spectrum_batch_size" to something non-zero. If this parameter value is set to 0, Comet will try to load all spectra into memory at once. With y

Re: [spctools-discuss] Query regarding searching in Comet in TPP

There is an issue with your comet.params file per the error message for the Comet search. Can you confirm the comet.params file is a plain text file? Also if you did any editing of this file in Word or whatever text editor you used, make sure any line wrapping is disabled. If you continue to have

Re: [spctools-discuss] SQT file to text file

erting my code to C# code . But Not able to read that > file. Please find attached file here. > > On Wednesday, January 18, 2017 at 10:54:03 PM UTC+5:30, Jimmy Eng wrote: >> >> *.sqt files are just plain text files containing MS/MS search >> identifications. >>

Re: [spctools-discuss] SQT file to text file

*.sqt files are just plain text files containing MS/MS search identifications. Here's a page describing the format: http://crux.ms/file-formats/sqt-format.html Here's the original publication describing the file: https://www.ncbi.nlm.nih.gov/pubmed/15317041 On Wed, Jan 18, 2017 at 3:49 AM, gaura

Re: [spctools-discuss] Re: Install TPP v5.0.0 on Ubuntu 16.04.1 LTS Linux

I found the offending code causing the buffer overflow issue in InteractParser.cpp and committed the fix to trunk (revision 7460). On Thu, Nov 17, 2016 at 2:12 PM, Roden Luo wrote: > Sorry guys, there are problems by installing TPPv5 in this way. > > 1. I cannot run comet, the same problem as de

Re: [spctools-discuss] Re: pepXML: aminoacid_modification elements in search_summary

To address Harald's point, we should simple add something like "static" and "variable" attributes to the "mod_aminoacid_mass" elements as below. I think it makes a lot of sense to do something like this especially if we're going to be adding other (optional?) attributes such as "source".

Re: [spctools-discuss] Multi core analysis

see > if I can obtain shorter analysis time. > > Thanks, Eslam > > On Wed, Aug 10, 2016 at 7:54 AM, Jimmy Eng wrote: > >> How much memory/RAM do you have on your computer? It won't make a huge >> difference but larger spectrum batch sizes are more efficient. So

Re: [spctools-discuss] Multi core analysis

hosphorylations were defined). I have also > confined the analysis to 1000 spectra batch size. Database search takes a > long time, but it identifies a large number of microbiome proteins with > high confidence. > > Eslam > > On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng wrote: &

Re: [spctools-discuss] Multi core analysis

Eslam, Setting "num_threads = 0" is the best you can do. There's no free lunch ... a database that's 100 times larger than the human UniProt fasta will take approximately 100 times longer to run, e.g. a 10 minute human search would translate to a 17 hour search if the database were 100 times larg

Re: [spctools-discuss] Difference between mxML and mzXML format

5% > 5% 5% 5% 5% 5% 5% 5% 5% 5% 5% > 5% 5% 5% 5% 5% 6% > - Post analysis: done > > Search end: 06/22/2016, 12:02:00 PM > > On Wednesday, June 22, 2016 at 2:09:27 AM UTC+5:30, Jimmy Eng wrote: >

Re: [spctools-discuss] Difference between mxML and mzXML format

Vijay, The likely reason you're seeing differences in spectrum counts loaded by Comet is that you have different data in the converted files. It's not an issue with the two formats nor Comet but that the converted data is different in your two files. Fix that and you'll see the two formats give

Re: [spctools-discuss] Comet database search error

es in your Ubuntu install. On Sun, Jun 12, 2016 at 11:49 PM, 钟传奇 wrote: > Hi Jimmy, > > I also want to ask how to update Comet in TPP in Ubuntu system. Does Comet > work if I just replaced the Comet file like you mentioned in the email. > > Thanks. > > > On Mon, Ju

Re: [spctools-discuss] Comet database search error

Vijay, Update to the latest Comet and try again. There's a good chance it won't solve your problems but there's no point in investigating search issues for a version of Comet (release 2014.02 rev. 2) that's outdated by nearly 2 years. To update your Comet binary, go to comet-ms.sourceforge.net a

Re: [spctools-discuss] condition.xml for TMT10plex

The fourth link under the "Miscellaneous" section on this page has a zip file containing a selection of Libra condition.xml files including what we use for TMT 10-plex: http://proteomicsresource.washington.edu/protocols06/ On Fri, Apr 1, 2016 at 12:46 PM, Shiliang Wang wrote: > Hi, All: > >

Re: [spctools-discuss] Comet search performance issue

A related weird part is that it looks like it's looking for (and presumably writing) the output here: c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml even though the input data was in c:\Inetpub\wwwroot\ISB\data\mydata\ On Tue, Mar 22, 2016 at 12:03 PM, Luis Mendoza < luis.mend..

Re: [spctools-discuss] Comet search performance issue

I was also puzzled by > that myself. I clearly selected the input file (mydata.pep.xml) from a > valid folder. I am going to try to do it from the command line using the > "cheat" method that Brian suggested earlier. > > Thanks, > > Bob > > On Tuesday, March 22, 2

Re: [spctools-discuss] Comet search performance issue

t; > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown error >

Re: [spctools-discuss] Comet search performance issue

0., mono. > 0.0 > add_X_user_amino_acid = 0. # added to X - avg. 0., mono. > 0.0 > add_Z_user_amino_acid = 0. # added to Z - avg. 0.0000, mono. > 0.0 > > # > # COMET_ENZYME_INFO _must_ be at the end of this parameters file > # >

Re: [spctools-discuss] Comet search performance issue

It would be helpful if you post (or send me) the search parameters which is the contents of the comet.params file. On Mon, Mar 21, 2016 at 2:11 PM, wrote: > Hi everyone, > > I started a Comet search in TPP three days ago and it is still going three > days later. I must have messed up something w

Re: [spctools-discuss] Possible to run either msconvert or ReAdw on Linux using WINE?

Report back if you somehow get it to work. I was under the impression that Visual Studio 2013 has a "garbage" rating with Wine compatibility. A dev. here compiled msconvert using the VS2010 revision right before the pwiz project moved over to VS2013 and we can get that running under Wine but it w

Re: [spctools-discuss] Re: Libra quantification

Actually for both of you, your best bet is to start with the mzML file that you generate from your mgf using msconvert. Search that with your search tool of choice and then run Libra. That should work. -- You received this message because you are subscribed to the Google Groups "spctools-discu

Re: [spctools-discuss] Re: Libra quantification

The problem is due to starting out with the mgf file. Libra and the TPP tools needs to know which spectrum/scan in the mgf/mzML file is associated with which identification. So there needs to be some type of convention in how the mgf file annotates this which means you can't start with just any m

Re: [spctools-discuss] readmzXML, tandem, and comet fail with files larger than 2 GB

ll be 32-bit (unless I >> misunderstand something) and as far as I know, there's no way to tell gcc >> to substitute int64 for int. >> >> If there aren't any ideas on where to start in the codebase, I'll start >> digging in with gdb >> >>

Re: [spctools-discuss] readmzXML, tandem, and comet fail with files larger than 2 GB

t compiler on a 64-bit system your int will still be 32-bit (unless I > misunderstand something) and as far as I know, there's no way to tell gcc > to substitute int64 for int. > > If there aren't any ideas on where to start in the codebase, I'll start > digging in with

Re: [spctools-discuss] readmzXML, tandem, and comet fail with files larger than 2 GB

Daniel, The issue you're seeing might be due to TPP windows programs compiled as 32-bit binaries. The first thing I'd try is grabbing a 64-bit binary of one of the tools to see if that fixes things. You can grab a 64-bit Comet binary from its SourceForge download site if you want to test this.

Re: [spctools-discuss] Sequest on TPP

There is no Sequest distributed with the TPP. This means you will need to get the parameters file from your Sequest installation (that is hopefully still compatible with the TPP). Or better yet make life easier for your self and simply use X!Tandem or Comet, both of which are distributed with the

Re: [spctools-discuss] Dimethylation labeling analysis using Coemt

You have 6 parameter values for your "variable_mod04" entry and 7 parameter values for your "variable_mod05" entry. One of them is wrong. variable_mod04 = 6.03181 K 0 3 -1 0 variable_mod05 = 6.03181 n 0 3 0 2 0 As you mentioned the heavy lysines are identified correctly, you might also jus

Re: [spctools-discuss] MS3 quantification

Libra, the TPP's tool for quantifying TMT/iTRAQ data, will now work with MS3 quantification. Make sure you're using the latest TPP and have this setting in your Libra condition file: On Tue, Jul 7, 2015 at 8:19 AM, hh1985 wrote: > Hi all, > > I have some TMT10plex datasets using MS3 for qu

Re: [spctools-discuss] TPP-4.8.0 compilation error (Linux 64bit): undefined reference to `gdImagePngPtr'

Based on googling , my best guess would be your libgd was compiled without PNG support. On Tue, Jun 2, 2015 at 4:55 PM, Robert wrote: > Hi, I just enjoyed a personal building workshop at the ASMS with David and > Luis, > > However, we are not able to build the TPP 4.8.0 on Fatdog64 ( > http://di

Re: [spctools-discuss] Re: Any tips on how to analyzed triple labeled data?

I can get xpress working with L/M/H SILAC. But I loath the thought of the work it would take to interface it within the TPP (updating pepXML schema, xinteract wrapper tool, XPressPeptideRatioParser, XPressProteinRatioParser, PepXMLViewer, the protein viewer, etc.). I will play with my standalone,

Re: [spctools-discuss] Anyone know some way to convert mascote format (mass) to Fasta?

The Mascot format, Mascot generic file or MGF, represents spectra. The FASTA format is used to represent sequences. They are two different things and it doesn't make sense to want to convert one to the other. Figure out what you really need and possibly follow-up here. On Wed, Apr 29, 2015 at 1

Re: [spctools-discuss] how to continue or kill my jobs?

in\) with > comet.2014010.win64.exe > from the zip,and rename it to "comet.exe". > Surprisedly, as I restarted TPP and performed comet, it run well and > completely! I clicked the "refresh" and it showed "search end" and "command > successful"! >

Re: [spctools-discuss] how to continue or kill my jobs?

e = 5000 > > > I perform TPP on win7(64bit) with 16G memory... > > 在 2015年4月15日星期三 UTC+8下午1:08:02，Jimmy Eng写道： >> >> Is this high-res MS/MS data? If so, what are your settings for the >> following Comet search parameters? >> >>fragment_bin_tol

Re: [spctools-discuss] how to continue or kill my jobs?

Is this high-res MS/MS data? If so, what are your settings for the following Comet search parameters? fragment_bin_tol use_sparse_matrix spectrum_batch_size And how much memory (RAM) does your computer have? - Jimmy On Tue, Apr 14, 2015 at 7:47 PM, c qin wrote: > Thanks for your at

Re: [spctools-discuss] Re: spectrast fail on comet pep.xml

Unfortunately I can't help you with Mayu as it's not a tool I use. You might consider re-posting your attachment as only a small portion of the top of the image is visible. On Wed, Mar 11, 2015 at 10:58 PM, Rachel wrote: > HI David and Jimmy, > > It worked after removed ./. Thank you so much! >

Re: [spctools-discuss] sqt2xml error from Sequest or ProLuCID in IP2 for TPP

ub/wwwroot/ISB/data/HBrainCIDHwang/20111216_CON_PE_01/20111216_CON_PE_01.08642.08642.2.dta> > 8642 [unavailable] *[spectrum]* > <http://localhost/tpp-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=1&PepMass=1472.23&Isobaric=1&Pep=&Dta=c:/Inetpub/wwwroot/IS

Re: [spctools-discuss] Re: spectrast fail on comet pep.xml

Rachel, I was able to run a Comet search through creating a SpectraST library so I took a look at your posted comet.iprohpet.pep.xml file and the problem is that, for some reason, your spectrum names are off. They look like wrote: > Hi Jimmy, > > I just run spectrast in C:\inetpub\wwwroot\I

Re: [spctools-discuss] sqt2xml error from Sequest or ProLuCID in IP2 for TPP

Anyways, let me know if you need me to follow-up with this any further. - Jimmy On Mon, Mar 9, 2015 at 8:55 PM, Heeyoun Hwang wrote: > Ok, I sent the files to you. > > thx. > > Heeyoun > > 2015년 3월 10일 화요일 오전 2시 22분 11초 UTC+9, Jimmy Eng 님의 말: >> >> Can you

Re: [spctools-discuss] Re: spectrast fail on comet pep.xml

Rachel, It looks like you ran the search in C:\inetpub\wwwroot\ISB\data\Dengue_comet\ but SpectraST is looking for the mzXML files in C:\Users\Administrator\Dengue\ The change in directory is the issue and is a little odd. You should try either of these possible solutions: - run iProph

Re: [spctools-discuss] sqt2xml error from Sequest or ProLuCID in IP2 for TPP

Can you make the SQT and sequest.params file available to me? Either email it to me directly or make it available for download. I'll take a quick look to see what's happening. The mzXML/mzML file is optional; it will write instrument info into the resulting pep.xml if present. - Jimmy On Sun,

Re: [spctools-discuss] bad allocation

See the replies in these threads: https://groups.google.com/forum/#!topic/comet-ms/RvcCr7j9m64 https://groups.google.com/forum/#!topic/comet-ms/ePVEULkA0kM https://groups.google.com/forum/#!topic/spctools-discuss/Q5lX6fLb1xo And the notes page on the Comet website: http://comet-ms.sourceforge.ne

Re: [spctools-discuss] translateDNA2AA-FASTA

l it be recognized by the data base search > function? > > Veronica > > On Friday, October 24, 2014 4:27:44 PM UTC-4, Jimmy Eng wrote: >> >> The binary is included with the TPP distribution but I don't believe that >> you can access it in the TPP's web interfa

Re: [spctools-discuss] translateDNA2AA-FASTA

The binary is included with the TPP distribution but I don't believe that you can access it in the TPP's web interface. So you're going to have to run it in a command prompt. Here's an example set of instructions that'll hopefully work for you: 1. Create a directory named c:\translate 2. Put

Re: [spctools-discuss] Mascot2XML - no enzyme

use "-Enonspecific" If you just type "Mascot2XML" without any other input arguments, it will list out the command line arguments including the recognized enzyme options. On Tue, Oct 7, 2014 at 12:37 PM, Vishal Swaroop wrote: > Hi, > > Is there a way to specify no enzyme for Mascot2XML executab

Re: [spctools-discuss] X!tandem error

I don't know what the issue is with X!Tandem but just wanted to comment on an unrelated issue which is that you should think twice about using X!Tandem's refinement mode, especially if you are going to push those search results through PeptideProphet or even simple target-decoy FDR. All proteins t

Re: [spctools-discuss] How to process MS3 Data from Orbitrap Fusion?

To search MS3 spectra in Comet, you need to set the parameter "ms_level = 3". Typically the value of that parameter is set to "2" for MS/MS scans. http://comet-ms.sourceforge.net/parameters/parameters_201402/ms_level.php Although a few of the ProteoWizard devs are here too, you might consider

Re: [spctools-discuss] TPP translation code is wrong.

Add "Wrong in what way i.e. why do you think the translation code is wrong?" Any translation is being done using the universal genetic code. On Tue, Jul 22, 2014 at 6:12 PM, Luis Mendoza < luis.mend...@systemsbiology.org> wrote: > Hello Rachel, > What tool were you using? What was the input da

Re: [spctools-discuss] Re: Base peak intensity values not reported in pepxml files

Brian, That "-PREC" command line option in "xinteract" will invoke the "-I" option in "InteractParser" to report the precursor intensity. "xinteract" is a wrapper that runs many tools, including "InteractParser" that Jason referred to. Hope this makes sense. - Jimmy On Thu, Jul 17, 2014 at 3:

Re: [spctools-discuss] TPP translation code

The translateDNA2AA.exe program uses the standard genetic code to translate nucleotides to amino acids; I don't use tblastn but would have to assume that it uses the same translation table. On Tue, Apr 29, 2014 at 3:12 AM, Hannes Röst wrote: > Hi Rachel > > sorry, I dont know enough about the T

Re: [spctools-discuss] Sqt2XML error

t; > > On Tue, Apr 15, 2014 at 3:05 PM, Jimmy Eng wrote: > >> Will, >> >> Can you send me a copy of your cidtest.sqt file and I'll look into it >> when I get a chance? Compress/zip the 11Mb file and either email it to me >> or make it available as a do

Re: [spctools-discuss] Sqt2XML error

Will, Can you send me a copy of your cidtest.sqt file and I'll look into it when I get a chance? Compress/zip the 11Mb file and either email it to me or make it available as a download link. Thanks. - Jimmy On Tue, Apr 15, 2014 at 11:30 AM, Will Fondrie wrote: > > I've been playing around w

Re: [spctools-discuss] Can XInteract support MSGF+?

I believe that PeptideProphet failed because you told it to use a decoy tag that it could not find in any of the search results. Apparently the decoy tag in MSGF+ is always "XXX_" and can't be changed. So you must set that as the decoy tag and make sure that same decoy tag is used in MyriMatch.

Re: [spctools-discuss] XPRESS values

Oliver, The Xpress chromatogram viewer lags Xpress in functionality and because of this, can report a different ratio. There was functionality added to Xpress which impacts the chromatogram reconstruction, such as the -p isotope option, which never made it to the Xpress viewer. So both tools can

Re: [spctools-discuss] Comet

Mar 4, 2014 at 2:12 AM, magnus.palmb...@gmail.com < magnus.palmb...@gmail.com> wrote: > Hi Jimmy, > > Many thanks - the "spectrum_batch_size" trick worked! Are the results > (e.g. the expectation values) dependent on the batch size? > > > Cheers, > > Magnus >

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