Peptide Mass Fingerprinting

[KlaraSc]

Hi there,

I am doing an on-tissue digestion followed by MALDI-MS analysis. No LC/MS. My resulting peak list contains MS1 m/z values for all masses detected. No MSMS is performed.

Is it possible to use searchGUI and peptide shaker to assign these MS1 m/z values to possible peptide fragments resulting from protein digestion? (something like MASCOTS Peteide Mass Fingerprint search)

I tried playing around with it and uploaded my list as mgf but it fails as I obviously have no precursor ion and MSMS files available?

thank you very much,

Kind regards, Klara

[mvaudel]

Hi Klara,

I am sorry but we don't support peptide mass fingerprinting. Unless you have a very simple mixture, the peptide mass is not sufficient to have a unique match in the database. When looking at precursors from a HeLa run with the simplest search settings (high resolution, only oxidation of methionine as modification, canonical human sequences), you already end up having 99.3% of your precursors mapping to more than one peptide. In average, a precursor maps to more than 1000 possible peptides, as shown on the histogram below.

Most of these peptides would not match even a single ms2 peaks and therefore get quickly discarded by search engines. This is why everyone does MS/MS these days.

Hope this helps!

Marc

[KlaraSc]

Hi Marc,

That is a pity. Indeed, I understand that MSMS is required and I will run MSMS on some peaks but I cannot do it on all, thus I wanted to narrow my focus on potential candidate peaks with some meaning to us. 

Thank you for your reply,

kind regards,

Klara

---------- Původní zpráva ---------- Od: Marc Vaudel notifications@github.com Komu: compomics/peptide-shaker peptide-shaker@noreply.github.com Datum: 13. 12. 2016 10:15:03 Předmět: Re: [compomics/peptide-shaker] MS1 peptide m/z search . HELP (# 234)

" Hi Klara,

I am sorry but we don't support peptide mass fingerprinting. Unless you have a very simple mixture, the peptide mass is not sufficient to have a unique match in the database. When looking at precursors from a HeLa run with the simplest search settings (high resolution, only oxidation of methionine as modification, canonical human sequences), you already end up having 99.3% of your precursors mapping to more than one peptide. In average, a precursor maps to more than 1000 possible peptides, as shown on the histogram below.

precursorhistogram (https://cloud.githubusercontent.com/assets/11632644/21134079/6cb36bae-c11c-11e6-971f-8b147b0fcbb4.png)

Most of these peptides would not match even a single ms2 peaks and therefore get quickly discarded by search engines. This is why everyone does MS/MS these days.

peakshistogram (https://cloud.githubusercontent.com/assets/11632644/21134147/d0cdd62e-c11c-11e6-953a-d0d4c341e6b4.png)

Hope this helps!

Marc

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub (https://github.com/compomics/peptide-shaker/issues/234#issuecomment-266685838) , or mute the thread (https://github.com/notifications/unsubscribe-auth/AXYkAh1evD90pnTLL6_e1TCT_l3p7bJKks5rHmITgaJpZM4LKSsZ) .

"

[mvaudel]

Hi again,

If it can help, I will keep my eyes open for tools that allow mapping the potential peptides for a given precursor and come back to you when I find something. In the meantime if you agree I will close this issue as it is not really related to PeptideShaker because we focus on MS/MS there.

Best regards,

Marc

[KlaraSc]

Hey,

yes of course close it.

And thanks for looking out, however, my intention was to compare several platforms and peptide shaker was one on my list. I know that MASCOT does what I need a well as MS-FIT. They just don't have it as nicely worked out, mainly the visualization part, as you do. So I wanted to compare their performance and use the  best one.

cheers,

Klara

---------- Původní zpráva ---------- Od: Marc Vaudel notifications@github.com Komu: compomics/peptide-shaker peptide-shaker@noreply.github.com Datum: 13. 12. 2016 17:22:04 Předmět: Re: [compomics/peptide-shaker] Peptide Mass Fingerprinting (#234)

" Hi again,

If it can help, I will keep my eyes open for tools that allow mapping the potential peptides for a given precursor and come back to you when I find something. In the meantime if you agree I will close this issue as it is not really related to PeptideShaker because we focus on MS/MS there.

Best regards,

Marc

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub (https://github.com/compomics/peptide-shaker/issues/234#issuecomment-266784566) , or mute the thread (https://github.com/notifications/unsubscribe-auth/AXYkAkFwacs6oHNTQ3tO2WHKpY_gFOclks5rHsYpgaJpZM4LKSsZ) .

"