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** Use "Format \-> Conditional formatting" to open the dialog box
** In the pop-up dialog box, click "Text contains" and change it to "Greater than", enter "9" in the box next to "Greater than", click on the box to the right of "Background" and select your favorite highlight color
* Use ProteoSAFe results filters to assess whether you would choose the mass offset as a realistic modification - MODa search results in the "Group by Peptide" view: [http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bf10de33c7c648f5941a682bf85bc585&view=group_by_peptide_old] modification.
** Example: GEMFILE(K,58)GEYPR, see [variants of this peptide|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bcc870f7e3ed4fc5a8ff95d50807b4c5&view=group_by_modified_peptide_overall#%7B%22Processed_peptide_input%22%3A%22GEMFILEKGEYPR%22%7D] or see [spectral network|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?view=network_displayer&componentindex=749&task=bcc870f7e3ed4fc5a8ff95d50807b4c5#%7B%7D]
** *{+}Question:+* Is M+58DIAIHHPWIR N-term real?
*** MOD peptides: see [variants of M 58DIAIHHPWIR|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bf10de33c7c648f5941a682bf85bc585&view=group_by_peptide_old#%7B%22Peptide_input%22%3A%22AIHHPWIR.%22%7D] (see [all peptides|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bf10de33c7c648f5941a682bf85bc585&view=group_by_peptide_old#%7B%7D])
*** Multi-pass peptides: see [variants of M 58DIAIHHPWIR|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bcc870f7e3ed4fc5a8ff95d50807b4c5&view=group_by_modified_peptide_overall#%7B%22Processed_peptide_input%22%3A%22MDIAIHHPWIR%22%7D] (see [all peptides|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bcc870f7e3ed4fc5a8ff95d50807b4c5&view=group_by_modified_peptide_overall#%7B%7D])
* Observations that reinforce confidence in observed mass-shifts
** Mass shift corresponds to known PTM on indicated amino acid (see [Unimod|http://www.unimod.org/modifications_list.php?pagesize=500] , login as "guest" if asked to)
*** *{+}Question:+* what *{+}Question:+* What amino acids can have a modification of \+58 Da? Which are biological and which could be sample-processing artifacts?
*** *{+}Example 1:+*  Is GEMFILE(K,58)GEYPR real? See [variants of this peptide|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bcc870f7e3ed4fc5a8ff95d50807b4c5&view=group_by_modified_peptide_overall#%7B%22Processed_peptide_input%22%3A%22GEMFILEKGEYPR%22%7D] or see [spectral network|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?view=network_displayer&componentindex=749&task=bcc870f7e3ed4fc5a8ff95d50807b4c5#%7B%7D]
*** *{+}Example 2:+* Is M+58DIAIHHPWIR N-term \+58?
**** MOD peptides: see [variants of M 58DIAIHHPWIR|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bf10de33c7c648f5941a682bf85bc585&view=group_by_peptide_old#%7B%22Peptide_input%22%3A%22AIHHPWIR.%22%7D] (see [all peptides|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bf10de33c7c648f5941a682bf85bc585&view=group_by_peptide_old#%7B%7D])
**** Multi-pass peptides: see [variants of M 58DIAIHHPWIR|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bcc870f7e3ed4fc5a8ff95d50807b4c5&view=group_by_modified_peptide_overall#%7B%22Processed_peptide_input%22%3A%22MDIAIHHPWIR%22%7D] (see [all peptides|http://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?task=bcc870f7e3ed4fc5a8ff95d50807b4c5&view=group_by_modified_peptide_overall#%7B%7D])
** PSMs with overlapping sequences help reinforce PTM IDs, especially if the same PTM occurs on the same site on different peptides
** Look for same identification with multiple precursor charge states
** Look for correlated peptide fragmentation intensities between multiple peptide variants (same sequence, different mass shifts)
** *{+}Question:+* is the \+58 Da mass offset a real modification on the N-term of protein gi\|117385?
*** Enter "gi\|117385" in the filter box for "Protein"
*** Enter "1~11" in the filter box for "Peptide Position" (to get only peptides starting at amino acid 1 and ending at amino acid 11)
*** Click the "Filter" button at the top left of the results table
*** Analyze the protein N-term at the bottom of the table
* Common artifacts in mass-shift frequency tables
** Site localization is especially inaccurate for blind searches because all amino acids are accepted as modification sites for all modifications