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

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

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 know what "normal

[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

Re: [spctools-discuss] XPRESS peak intensity value

cursor_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 intensity >> a

Re: [spctools-discuss] XPRESS peak intensity value

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 4:32:25 PM UTC

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 >

[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

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:

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

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

[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

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

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

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

> > 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 >> seeing a d

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

n > 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 have completed fine. The &

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

ot;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 there something els

[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

[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

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

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, Apr 13,

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

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

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 search

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

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

uot; 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_methionine'

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

[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.

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,

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".

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

em search to run. > > 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 >> compare

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

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

os are correct. > 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, Ji

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

lease candidate that 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 hope

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 >

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 <jke...@gmail.com> 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

[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:

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

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

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: >

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

Re: [spctools-discuss] Re: Libra quantification

reason? I actually 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, 201

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

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

gt; PASCAL. Now I am converting 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 >> ident

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,

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,

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

1 spectra batch size to see > if I can obtain shorter analysis time. > > Thanks, Eslam > > On Wed, Aug 10, 2016 at 7:54 AM, Jimmy Eng <jke...@gmail.com> wrote: > >> How much memory/RAM do you have on your computer? It won't make a huge >> difference but larger spe

Re: [spctools-discuss] Multi core analysis

methionine oxidation or phosphorylations 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

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

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

4% 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

> On Mon, Jun 13, 2016 at 2:24 PM, Jimmy Eng <jke...@gmail.com> wrote: > >> 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 versio

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

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

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 <

Re: [spctools-discuss] Comet search performance issue

out by the system. 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 Tu

Re: [spctools-discuss] Comet search performance issue

in 0 sec > > 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.

Re: [spctools-discuss] Comet search performance issue

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., mono. > 0.0 > > # > # COMET_ENZYME_INFO _must_ be at the end of this parameters file > # > [COMET_ENZYME_IN

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

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

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

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

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

ler 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 gdb

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

a > 64-bit 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] 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 just

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: reporterFromMS3 value=1 / On Tue, Jul 7, 2015 at 8:19 AM, hh1985 hh.earlyd...@gmail.com wrote: Hi all, I

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 robert.wink...@bioprocess.org 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

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

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

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 cco...@gmail.com wrote:

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 rachel2005...@gmail.com wrote: HI David and Jimmy, It worked after removed ./.

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

to your seminar. :) 2015년 3월 11일 수요일 오전 1시 5분 44초 UTC+9, Jimmy Eng 님의 말: Heeyoun, I was able to run the sqt2xml program on your sqt file fine. The sqt file you sent me is a little worrisome (see below) but the conversion to pepXML did work. Can you tell me what didn't work for you

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

if you need me to follow-up with this any further. - Jimmy On Mon, Mar 9, 2015 at 8:55 PM, Heeyoun Hwang tilldaw...@gmail.com 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 make the SQT and sequest.params file available

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

Re: [spctools-discuss] translateDNA2AA-FASTA

? 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 interface. So you're going to have to run it in a command prompt. Here's an example set of instructions

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] 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] 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 3:19 PM,

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 hannesro...@gmail.com wrote: Hi Rachel sorry, I dont know

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 fondr...@gmail.com wrote: I've been

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

, 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 On Monday, 3 March 2014 19:05:21 UTC+1, Jimmy Eng wrote

Re: [spctools-discuss] Comet

Mangus, There's something broken with our latest Comet 2013.02 rev. 2 release under Windows. We attempted to address large memory search performance, which appeared to work fine in our limited testing, but we definitely broke something else in the process and are actively working on addressing

Re: [spctools-discuss] Question on setting modifications for searching

This question comes up semi-regularly; here's the explanation obtained from the author of X!Tandem many years ago: http://tools.proteomecenter.org/wiki/index.php?title=TPP:X!Tandem_and_the_TPP#X.21Tandem_default_modifications On Sat, Feb 15, 2014 at 12:04 AM, Konstantinos Vougas

Re: [spctools-discuss] Decoy issue

The decoy tag/names need to be the prefix i.e. REVERSED_sw|P84710| In this example, enter REVERSED_ in the input text box. There's no way to do it with your existing decoy notation format so you are unfortunately going to need to change your decoy entry names. On Sun, Jan 19, 2014 at 5:27 PM,

Re: [spctools-discuss] How to calculate offset for each scan in mzXML file

Here's a useful document to look through if you haven't seen it yet: http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/Doc/mzXML_2.1_tutorial.pdf SHA is an acronym for secure hash algorithm and the sha1 element is described in section 7 of the document above. It is a hash value

Re: [spctools-discuss] How to calculate offset for each scan in mzXML file

Each index offset is the number of bytes from the beginning of the file for each scan. You can use something like the ftell function to return this value for a file pointer that is pointing to the opening character of each scan element. On Fri, Dec 13, 2013 at 10:09 PM, Jorey Dong

Re: [spctools-discuss] Unable to process comet.2012013.win64.exe output with peptide prophet

Are there peptide IDs in your 54ProtMix_S1R1.pep.xml file? The error message is suggesting that there aren't any. If you don't know how to tell, you can email me that pep.xml file and I'll take a look. - Jimmy On Fri, Sep 27, 2013 at 10:32 PM, Punit Kadimi itspuni...@gmail.com wrote: Hello

Re: [spctools-discuss] Unable to process comet.2012013.win64.exe output with peptide prophet

Puneet, https://groups.google.com/forum/#!topic/comet-ms/jUhIR5zWWcU For Comet support, you need to be using TPP version 4.6.2 or newer. The current release is 4.6.3. You're current running 4.5.2. I just ran PeptideProphetParser from version 4.6.3 on your file and it processed fine. - Jimmy

Re: [spctools-discuss] label free quantitation by xpress

algorithm: xpressratio_summary version=2.1 (TPP v4.5 RAPTURE rev 2, Build 201307022022 (linux)) author=Jimmy Eng same_scan_range=Y labeled_residues=MLIGHT xpress_light=0 massdiff=MLIGHT,1.00 masstol=0.05 min_num_chromatogram_points=6 min_num_isotope_peaks=0/ My questions are: 1. Basically -M

Re: [spctools-discuss] XTandem and k-score

)’: mscore_k.cpp:371:36: error: ‘m_vmiType’ was not declared in this scope make: *** [mscore_k.o] Error 1 Thanks, Rishika On Thu, Jul 25, 2013 at 4:44 PM, Jimmy Eng jke...@gmail.com wrote: You would need a version of X!Tandem that has k-score in it so use the one distributed with the TPP

Re: [spctools-discuss] Matched ions in x!tandem

I can give you a command line tool to dump this information from a pep.xml file easily. Just let me know if you want a windows or linux binary (or the C source file) and what other information in the pep.xml file you want exported. On Wed, Jul 24, 2013 at 5:50 PM, Bosco Ho appos...@gmail.com

Re: [spctools-discuss] eliminate fixed modification numbers in pep.xml

Tony, As far as I'm aware, there's no simple way to accomplish what you want to do i.e. there's no option or switch in the TPP tools to turn off the fixed mod masses but leave the variable mod masses in the peptide string. If this is just a question of getting rid of those fixed mod masses in

Re: [spctools-discuss] TMT data analysis

The spectrum viewer has nothing to do with your database search i.e. it knows nothing about how you did a search and whether you applied a minimum fragment m/z or not. Nor does it know anything about TMT reporter peaks. It simply calculates fragment ions based on the peptide sequence and labels

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