spctools-discuss

1–30 of 3471

0 selected

sudarshan kumar

Sep 25

I need to acquisition settings for running silac samples (only heavy lysine (13 C6 and 15N2 and no argininge)

Hi can anyone please share or refer to me the aquisition settings and search settings/script for

unread,

I need to acquisition settings for running silac samples (only heavy lysine (13 C6 and 15N2 and no argininge)

Hi can anyone please share or refer to me the aquisition settings and search settings/script for

Sep 25

sudarshan kumar, mhoo...@systemsbiology.org6

Sep 25

Stpeter negative SIn value?

Ok Thank you. that makes sense. I should filter the list first before Stpeter quantitation. On

unread,

Stpeter negative SIn value?

Ok Thank you. that makes sense. I should filter the list first before Stpeter quantitation. On

Sep 25

Sanclayver Araújo

Sep 19

Good Morning! Does anyone know the link to download MASH explorer software? -- Sanclayver Corrêa

unread,

Good Morning! Does anyone know the link to download MASH explorer software? -- Sanclayver Corrêa

Sep 19

Jason Winget, David Shteynberg2

Sep 1

StPeter error - Could not read spectra

Hey Jason, If you are able to compress the dataset directory and share it I would be happy to

unread,

StPeter error - Could not read spectra

Hey Jason, If you are able to compress the dataset directory and share it I would be happy to

Sep 1

sudarshan kumar, mhoo...@systemsbiology.org2

Aug 16

1. No - see your other thread (https://groups.google.com/g/spctools-discuss/c/yDBVf5nHxmM) for a

unread,

1. No - see your other thread (https://groups.google.com/g/spctools-discuss/c/yDBVf5nHxmM) for a

Aug 16

Emma Whittington, Luis Mendoza3

Aug 7

converting prot.xml to tsv/something else

Thank you. A co-worker with a windows machine tried the ProtXMLViewer with the GUI. However, I'm

unread,

converting prot.xml to tsv/something else

Thank you. A co-worker with a windows machine tried the ProtXMLViewer with the GUI. However, I'm

Aug 7

Aug 4

Regarding protein prophet input - what difference does it make if I use PTM prophet file or not

And should I tick the "input is from iProphet" if I am using the PTM Prophet file generated

unread,

Regarding protein prophet input - what difference does it make if I use PTM prophet file or not

And should I tick the "input is from iProphet" if I am using the PTM Prophet file generated

Aug 4

sophie culos, … David Shteynberg7

Aug 1

Navigating peptideSieve Tips/Tricks?

Yes! I am doing everything in the bin directory for the test to make it easier to specify paths. My

unread,

Navigating peptideSieve Tips/Tricks?

Yes! I am doing everything in the bin directory for the test to make it easier to specify paths. My

Aug 1

Tanmay Singh, Luis Mendoza2

Aug 1

Problem with PeptideProphet

Hello Tanmay, How did you generate the input pepXML files? Which search engine did you use? Are you

unread,

Problem with PeptideProphet

Hello Tanmay, How did you generate the input pepXML files? Which search engine did you use? Are you

Aug 1

Debojyoti Pal, Luis Mendoza5

Aug 1

Variable mod query in COMET

I meant that they would come up with something to get it done with only variable modifications. By

unread,

Variable mod query in COMET

I meant that they would come up with something to get it done with only variable modifications. By

Aug 1

Aug 1

Regarding total intensity normalization in LIBRA

Can anyone help me with this, please? On Monday, July 31, 2023 at 11:39:47 PM UTC+5:30 Debojyoti Pal

unread,

Regarding total intensity normalization in LIBRA

Can anyone help me with this, please? On Monday, July 31, 2023 at 11:39:47 PM UTC+5:30 Debojyoti Pal

Aug 1

Carlo de Oliveira Martins, Luis Mendoza3

Jul 26

Access to Mascot file results

These are valuable tips. I will check if our Admin can open this port. Definitely, if I am able to

unread,

Access to Mascot file results

These are valuable tips. I will check if our Admin can open this port. Definitely, if I am able to

Jul 26

Luis Mendoza, … Luis9

Jul 21

Upcoming Trans-Proteomic Pipeline (TPP) course

Hello Sud, You can find some info and links to the download instructions and release notes at our

unread,

Upcoming Trans-Proteomic Pipeline (TPP) course

Hello Sud, You can find some info and links to the download instructions and release notes at our

Jul 21

suzmcde...@gmail.com, … Luis Mendoza8

Jul 18

Next proteomics informatics course?

Hi Don, We'll look into setting up a Zoom option and get back to you soon. Thank you for your

unread,

Next proteomics informatics course?

Hi Don, We'll look into setting up a Zoom option and get back to you soon. Thank you for your

Jul 18

muriell...@gmail.com, … David Shteynberg10

Jun 28

ProteinProphet output number of unique peptides vs total number of peptides

Hi Brian, I just confirmed in the code that it is counted here when the weight of the peptide is

unread,

ProteinProphet output number of unique peptides vs total number of peptides

Hi Brian, I just confirmed in the code that it is counted here when the weight of the peptide is

Jun 28

Emma Whittington, Luis Mendoza2

Jun 19

TPP Tandem input files

Hello Emma, According to this, X!Tandem is indeed able to process MGF files: https://www.thegpm.org/

unread,

TPP Tandem input files

Hello Emma, According to this, X!Tandem is indeed able to process MGF files: https://www.thegpm.org/

Jun 19

Jun 2

TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub

Hello everyone, Next week the TPP software tools team will be attending and giving several

unread,

TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub

Hello everyone, Next week the TPP software tools team will be attending and giving several

Jun 2

Sanclayver Araújo, … Jimmy Eng4

May 25

Proteome discoverer users guide

Thank you very much to all On Thu, 25 May 2023 at 14:07 Jimmy Eng <jke...@gmail.com> wrote: I

unread,

Proteome discoverer users guide

Thank you very much to all On Thu, 25 May 2023 at 14:07 Jimmy Eng <jke...@gmail.com> wrote: I

May 25

felipe velasquez, … Jimmy Eng5

May 5

protein validation

Dear Jimmy Thanks for your reply. I will use the correct database. Felipe El jue, 4 may 2023 a las 15

unread,

protein validation

Dear Jimmy Thanks for your reply. I will use the correct database. Felipe El jue, 4 may 2023 a las 15

May 5

Scott Starry, David Shteynberg2

May 5

Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022

Hello Scott, You should be able to get around this issue by unchecking the option to download and

unread,

Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022

Hello Scott, You should be able to get around this issue by unchecking the option to download and

May 5

May 4

TPP 6.3.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0 "Arcus" We are

unread,

TPP 6.3.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0 "Arcus" We are

May 4

felipe velasquez, Luis Mendoza5

Apr 29

Problem with PTMprophet

Thanks Luis for your quick response. Finally, I could resolve the problem. As a beginner user, I made

unread,

Problem with PTMprophet

Thanks Luis for your quick response. Finally, I could resolve the problem. As a beginner user, I made

Apr 29

Will Comstock, … Luis Mendoza5

Apr 7

SILAC quantification with targeted SIM

Hi Will, Glad you got this to work! A potentially quicker solution is to enter those extra flags in

unread,

SILAC quantification with targeted SIM

Hi Will, Glad you got this to work! A potentially quicker solution is to enter those extra flags in

Apr 7

Yasir Ahmed, Luis Mendoza6

Mar 28

Output sequence coverage info

Sure thing. And to answer your original question: there is a command-line tool in TPP called

unread,

Output sequence coverage info

Sure thing. And to answer your original question: there is a command-line tool in TPP called

Mar 28

felipe velasquez, … Eric Deutsch7

Mar 28

Hi Felipe, great! Yes, if you have questions, please post them to the list here. I may not always be

unread,

Hi Felipe, great! Yes, if you have questions, please post them to the list here. I may not always be

Mar 28

Aarthie Senathirajah

Mar 23

How does RT train work?

Hi I was wondering if there was a tutorial on how to use RT Train? I'm not sure what kind of

unread,

How does RT train work?

Hi I was wondering if there was a tutorial on how to use RT Train? I'm not sure what kind of

Mar 23

Priti Panchal, Eric Deutsch4

Feb 22

MSFragger param

ah, I see, okay, sure, I put one here: http://www.tppms.org/tmp/msfragger.params On Tue, Feb 21, 2023

unread,

MSFragger param

ah, I see, okay, sure, I put one here: http://www.tppms.org/tmp/msfragger.params On Tue, Feb 21, 2023

Feb 22

Feb 17

TPP 6.2.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are

unread,

TPP 6.2.0 Release is now available

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are

Feb 17

Aarthie Senathirajah, Luis Mendoza2

Feb 14

Analyzing Metaproteomic Data

Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know

unread,

Analyzing Metaproteomic Data

Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know

Feb 14

Jan 27

not getting significant hits while analyzing .raw file

Hi all, I have been trying to analyze .raw file generated on waters synapt of standard protein BSA

unread,

not getting significant hits while analyzing .raw file

Hi all, I have been trying to analyze .raw file generated on waters synapt of standard protein BSA

Jan 27

Search

Clear search

Close search

Google apps

Main menu