Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-12T01:51:19.563Z
Answers.Text: 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 ?
Answers.UserDisplayName: kevin
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-12T01:53:47.903Z
Answers.Text: and what do you exactly mean by **infobox of each residue** ?
Answers.UserDisplayName: kevin
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-12T09:24:41.660Z
Answers.Text: https://en.wikipedia.org/wiki/Mass-to-charge_ratio and https://en.wikipedia.org/wiki/Help:Infobox
Answers.UserDisplayName: Matteo Ferla
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-12T10:21:51.950Z
Answers.Text: May I ask why you specifically chose `ELVIS` ?  or was it just a demo example ?
Answers.UserDisplayName: kevin
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-12T10:23:04.287Z
Answers.Text: and I am not sure about **Does residue order matter for linear and backbone cyclised peptides? (Let's ignore isoaspartate etc.)**
Answers.UserDisplayName: kevin
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-12T12:46:37.853Z
Answers.Text: 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.
Answers.UserDisplayName: Matteo Ferla
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-09-03T10:43:05.480Z
Answers.Text: but there is difference between linear peptide and cyclic peptide (which is more difficult to solve) ?
Answers.UserDisplayName: kevin
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-09-03T11:41:15.960Z
Answers.Text: Wait, may I ask why would I need https://en.wikipedia.org/wiki/Mass-to-charge_ratio for this question ?
Answers.UserDisplayName: kevin
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-02T16:52:59.303Z
Answers.LastActivityDate: 2022-08-02T16:52:59.303Z
Answers.UserDisplayName: Matteo Ferla
Body: <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>
  
Tags: <proteins>
Title: mass spectrum matching with cyclic peptide and linear peptide
ThreadText: # 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?
  
  ```py
  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 ?  
  
  ---
  
  