<p>You are way overthinking this.</p>
<p>As this is homework I won't give any code, but I will throw back some questions:</p>
<ul>
<li>What is the definition of m/z?</li>
<li>Were the only tool available Wikipedia, could you simply read the infobox of each residue?</li>
<li>If so, what values would you need and what elements do you need to subtract?</li>
<li>Does residue order matter for linear and backbone cyclised peptides? (Let's ignore isoaspartate etc.)</li>
<li>Have you been introduced to RDKit in your course? E.g. what would this give you?</li>
</ul>
<pre class="lang-py prettyprint-override"><code>from rdkit import Chem
from rdkit.Chem import Descriptors
mol: Chem.Mol = Chem.MolFromFASTA('ELVIS')
print( Descriptors.ExactMolWt(mol) )
</code></pre>

CC BY-SA 4.0
2022-08-12T01:51:19.563Z
Sorry for late reply.  I am stucked with many other things last week.  I am new to `rdkit`, but  `print( Descriptors.ExactMolWt(mol) )` would give `559.32172802` , and what can I learn from this number ?
kevin
CC BY-SA 4.0
2022-08-12T01:53:47.903Z
and what do you exactly mean by **infobox of each residue** ?
kevin
CC BY-SA 4.0
2022-08-12T09:24:41.660Z
https://en.wikipedia.org/wiki/Mass-to-charge_ratio and https://en.wikipedia.org/wiki/Help:Infobox
Matteo Ferla
CC BY-SA 4.0
2022-08-12T10:21:51.950Z
May I ask why you specifically chose `ELVIS` ?  or was it just a demo example ?
kevin
CC BY-SA 4.0
2022-08-12T10:23:04.287Z
and I am not sure about **Does residue order matter for linear and backbone cyclised peptides? (Let's ignore isoaspartate etc.)**
kevin
CC BY-SA 4.0
2022-08-12T12:46:37.853Z
Demo. The amino acid sequence `ELVIS` is an ancient joke as it is very common, but `ELVISISALIVE` was not present in the draft human genome.
Matteo Ferla
CC BY-SA 4.0
2022-09-03T10:43:05.480Z
but there is difference between linear peptide and cyclic peptide (which is more difficult to solve) ?
kevin
CC BY-SA 4.0
2022-09-03T11:41:15.960Z
Wait, may I ask why would I need https://en.wikipedia.org/wiki/Mass-to-charge_ratio for this question ?
kevin
CC BY-SA 4.0
2022-08-02T16:52:59.303Z
2022-08-02T16:52:59.303Z
Matteo Ferla
<p>I was doing a simple quiz which I encountered the following two questions related to mass spectrum matching with cyclic peptide and linear peptide.</p>
<p>I have done some preliminary google search, but I am not sure how to use either  <a href="https://codereview.stackexchange.com/questions/193859/find-a-cyclic-peptide-with-a-given-non-ideal-spectrum">https://codereview.stackexchange.com/questions/193859/find-a-cyclic-peptide-with-a-given-non-ideal-spectrum</a> or <a href="https://github.com/rochoa85/pepfun" rel="nofollow noreferrer">https://github.com/rochoa85/pepfun</a> in this case.</p>
<blockquote>
<p>Which of the following cyclic peptides could have generated the
theoretical spectrum 0 71 101 113 131 184 202 214 232 285 303 315 345
416? (Select all that apply.)</p>
</blockquote>
<pre><code>TAIM

TMIA

MAIT

MTAI

TMLA

TLAM
</code></pre>
<blockquote>
<p>Which of the following linear peptides is consistent with Spectrum =
{0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332
333}? (Select all that apply.)</p>
</blockquote>
<pre><code>AVQ

TCQ

TVQ

QCV

TCE

ETC
</code></pre>

<proteins>
mass spectrum matching with cyclic peptide and linear peptide
# mass spectrum matching with cyclic peptide and linear peptide

(Asked by: username_0 on 2022-08-02)

I was doing a simple quiz which I encountered the following two questions related to mass spectrum matching with cyclic peptide and linear peptide.
I have done some preliminary google search, but I am not sure how to use either  https://codereview.stackexchange.com/questions/193859/find-a-cyclic-peptide-with-a-given-non-ideal-spectrum or https://github.com/rochoa85/pepfun in this case.

Which of the following cyclic peptides could have generated the
theoretical spectrum 0 71 101 113 131 184 202 214 232 285 303 315 345
416? (Select all that apply.)

TAIM

TMIA

MAIT

MTAI

TMLA

TLAM


Which of the following linear peptides is consistent with Spectrum =
{0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332
333}? (Select all that apply.)

AVQ

TCQ

TVQ

QCV

TCE

ETC

**Tags:** proteins

---

## 1 answers

### Answer by username_1 on 2022-08-02. Score: 3

You are way overthinking this.
As this is homework I won't give any code, but I will throw back some questions:

What is the definition of m/z?
Were the only tool available Wikipedia, could you simply read the infobox of each residue?
If so, what values would you need and what elements do you need to subtract?
Does residue order matter for linear and backbone cyclised peptides? (Let's ignore isoaspartate etc.)
Have you been introduced to RDKit in your course? E.g. what would this give you?

from rdkit import Chem
from rdkit.Chem import Descriptors
mol: Chem.Mol = Chem.MolFromFASTA('ELVIS')
print( Descriptors.ExactMolWt(mol) )

> **Comments:**
> **username_0**: Sorry for late reply.  I am stucked with many other things last week.  I am new to `rdkit`, but  `print( Descriptors.ExactMolWt(mol) )` would give `559.32172802` , and what can I learn from this number ?  
> **username_0**: and what do you exactly mean by **infobox of each residue** ?  
> **username_1**: https://en.wikipedia.org/wiki/Mass-to-charge_ratio and https://en.wikipedia.org/wiki/Help:Infobox  
> **username_0**: May I ask why you specifically chose `ELVIS` ?  or was it just a demo example ?  
> **username_0**: and I am not sure about **Does residue order matter for linear and backbone cyclised peptides? (Let's ignore isoaspartate etc.)**  
> **username_1**: Demo. The amino acid sequence `ELVIS` is an ancient joke as it is very common, but `ELVISISALIVE` was not present in the draft human genome.  
> **username_0**: but there is difference between linear peptide and cyclic peptide (which is more difficult to solve) ?  
> **username_0**: Wait, may I ask why would I need https://en.wikipedia.org/wiki/Mass-to-charge_ratio for this question ?  

---

