Summary Reports for MS/MS

At the completion of a search, a summary report is displayed that provides an overview of the results. There is a choice of report formats and all reports contain links to more detailed views of the experimental and calculated data.

For searches of less than 300 MS/MS spectra, the default summary report is the Peptide Summary. This provides a clear picture of the peptide matches, grouped into protein hits using a simple parsimony algorithm. If there are 300 or more spectra, the default summary report is the Protein Family Summary. This groups the proteins into families based on a novel hierarchical clustering algorithm and presents these results one page at a time, initially with 10 families per page. This report is ideally suited to very large and complex MS/MS searches, where it is not practical to display all the results on a single HTML page. For additional information about the Protein Family Summary, see Koskinen, V. R., Hierarchical Clustering of Shotgun Proteomics Data 2011 MCP 10 M110.003822

You can use the format controls to switch to a Select Summary, which is similar to a Peptide Summary, but provides a more compact view of the results. The Select Summary splits the peptide matches assigned to protein hits into a separate report from the unassigned peptide matches. For searches of less than 1000 MS/MS spectra, you can also choose a Protein Summary, but it is not recommended to do so unless you are viewing the results of a combination search. If the sample is a mixture, using one of the Protein Summary reports to view the results can give a very misleading picture.

If you are submitting MS/MS searches to an in-house Mascot server, and display the results as a Peptide Summary, you will also have the option to create an Archive Report. This is simply an edited version of the Peptide Summary report, that only includes the protein hits you have selected.

If there are no peptide sequence matches whatsoever from a search of MS/MS data, only molecular weight matches, then a Protein Summary report will be displayed. This indicates that the search has failed. Possibly the spectra are nothing but noise or possibly the search parameters are incorrect in some way.

Protein Family Summary

Sections of the report are described in the order in which they appear. Use this link to open an example report in a new browser window or tab.

(The Protein Family Summary makes extensive use of JavaScript and Scalable Vector Graphics. For full functionality, use a modern web browser with native SVG support. Further details on this page.)

Most of the information in a Family Summary is structured into sections that can be displayed or hidden. Links that toggle between the two states are easily recognised by the adjacent triangle. The triangle points to the right when the section is collapsed and points down when the section is expanded.

Header

At the top of the report are a few lines to identify the search uniquely: search title, date, user name, etc. The database version is identified with either a release number or an ISO datestamp.

A search can easily be repeated, so as to investigate the effect of changes in search parameters. The choices for repeating a search are set by radio buttons for All queries, Non-significant (below identity threshold), and Unassigned.

A drop-down list contains available export formats. Select the required format and choose Export. There is also a link to switch back to the earlier, Select Summary report, in case you are using some third party software application that only accepts the earlier report formats.

Search Parameters

The search parameters can be displayed or hidden by clicking on the sub-heading. Descriptions of individual search parameters can be found here.

Score Distribution

Histograms illustrating the peptide and protein score distributions can be displayed or hidden by clicking on the sub-heading.

The left hand histogram shows the peptide score distribution, divided into 16 bins. The heights of the bars show the number of matches in each bin.

Similarly, the right hand histogram shows the 50 highest protein scores. For a search of MS/MS data, protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. The protein score histogram has little meaning for MS/MS results, but is retained for historical reasons.

Modification statistics

This table lists the total number of instances of each modification found in significant matches. For an error tolerant search, a second column gives the counts for the error tolerant matches. This can be useful in judging whether any unsuspected modifications are so abundant that they should be selected as variable modifications for the first pass search.

Legend

A legend, explaining how font style and colour are used to convey information about individual peptide matches can be displayed or hidden by clicking on the sub-heading. Red indicates the top-ranking peptide match for the query. Bold indicates significant (score greater than homology threshold). Note that this meaning of bold is different from that used in the Peptide Summary and Select Summary. Italic font is used for a duplicate match (more than one query matches to the same peptide sequence with the same modifications, and charge state).

Format Controls

These controls enable the report format to be modified. After making changes, press the "Format As" button to reload the report using the new settings.

• Significance threshold The default significance threshold is p < 0.05. You can change this to any value in the range 0.99 to 1E-18.
• Maximum number of families This value was initially chosen when the search was submitted. Enter a positive integer if you wish to re-specify the number of protein families to report. Of course, the total number of families actually found by the search may be less. Entering the word AUTO or a value of 0 will display all of the families that have at least one peptide match with a significant score.
• Display non-significant matches When unchecked, only significant matches are displayed. This makes the report shorter and more readable. Check this box to display all matches, even those with low scores that may be false. (Note that this control can be replaced by an edit box that allows you to set an explicit expect value or score cut-off. For more information, search the Installation & setup manual for DisplayNonSignificantMatches.)
• Min. number of sig. unique sequences The default setting is 1, which means a family member could be a ‘one-hit wonder’. Setting a higher value will usually have a dramatic effect on the number of protein hits and the protein false discovery rate.
• Dendrograms cut at Causes all dendrograms to be cut at the specified score.

The following controls are only displayed for certain types of search:

• UniGene index (Only displayed for a search of a nucleic acid database when UniGene index files have been configured) Choose the UniGene index to be used to cluster the proteins into gene based families.
• Error tolerant matches (Only displayed for an automatic error tolerant search) A drop-down list can be used to switch between displaying both standard and error tolerant matches (the default), displaying just the standard matches, and displaying just the error tolerant matches.
• Show Percolator scores (Only displayed for searches that satisfy the requirements for using Percolator) Check to display scores and expect values adjusted by Percolator.
• Preferred taxonomy

If the search used a quantitation method specifying Multiplex or Reporter protocol, there will be an additional block of quantitation related controls, as described here. Checkboxes can be used to toggle the display of protein and peptide ratios.

If the search included the auto-decoy option, false discovery rate information is displayed in the final section of the header.

The body of the report consists of three tabs, one for protein families, one for Report Builder, and one for unassigned matches.

Protein Families

Proteins are grouped into families using a novel hierarchical clustering algorithm. If the family contains a single member, the accession string, protein score and description are listed. If the family contains multiple members, the accessions, scores and descriptions are aligned with a dendrogram, which illustrates the degree of similarity between members. To see complete information about the proteins in the family, and the peptide matches assigned to each family member, click on the family number link.

In the example result report, family 3 has 3 members. If necessary, to make the report as concise as possible, clear the checkbox for Display non-sig. matches (or set the Ions score or expect cut-off to 0.05) and choose Filter. This will remove all the low scoring matches. Now, expand family 3 by clicking on the family number link.

The dendrogram illustrates the degree of similarity between members of a protein family. The scale is ions score, and HSP7C_MOUSE and HS71L_MOUSE join at a score of approximately 30. This represents the score of the significant matches that would have to be discarded in order to make one protein a sub-set of the other. These two proteins are much more similar to one other than to BIP_MOUSE, which has non-shared peptide matches with a total score of approximately 145. Note that, where there are multiple matches to the same peptide sequence, (ignoring charge state and modification state), it is the highest score for each sequence that is used.

Immediately under the dendrogram is a list of the proteins. In this example, because SwissProt has low redundancy, each family member is a single protein. In other cases, a family member will represent multiple same-set proteins. One of the proteins is chosen as the anchor protein, to be listed first, and the other same-set proteins are collapsed under a same-set heading. There is nothing special about the protein picked for the anchor position. You may have a preference for one according to taxonomy or description, but all proteins in a same-set group are indistinguishable on the basis of the peptide match evidence.

Clicking on the accession string link will load a Protein View report. For each of the proteins, beside the protein score and mass, there are counts of the number of matches and the number of distinct sequences. In each column, the first number is the total count while the number in parentheses is the count for matches above the significance threshold. If you filtered the report to include only matches above the threshold, as suggested, the two numbers will always be the same.

To see the peptides that distinguish HSP7C_MOUSE and HS71L_MOUSE, clear the checkbox for BIP_MOUSE and choose Redisplay. The table of peptide matches will be reduced to rows and columns for just these two proteins, making it easier to compare the matches. A marker indicates that a particular peptide is found in a particular protein. It can be seen that HS71L_MOUSE would be a sub-set of HSP7C_MOUSE if it was not for one match, K.ATAGDTHLGGEDFDNR.L, which is present in HS71L_MOUSE and not in HSP7C_MOUSE. It is the significant score for this match that separates the two proteins in the dendrogram by a distance of 32 (score of 55 – homology threshold score of 23). If you look a little more closely, you will notice that K.STAGDTHLGGEDFDNR.M has a weak match in HSP7C_MOUSE. So, the evidence for both proteins being present comes down to a single residue. If S221 in HSP7C_MOUSE was an A, or A223 in HS71L_MOUSE was an S, then HS71L_MOUSE would be a sub-set protein. Interestingly, the stronger match is for the sequence found in the protein with fewer matches. This could be chance or it could be that the analyte sequence was essentially HSP7C_MOUSE but with an A at this position.

You can "cut" the dendrogram using the controls underneath. The slider control may not work in all browsers. If this is the case, you can type a numeric value into the threshold field. By using the slider or by entering a number, set the threshold to 50 and choose Cut. HS71L_MOUSE will be dropped from the dendrogram and the peptide match table because it is now a sub-set protein. If you compare the matches to HSP7C_MOUSE with those to BIP_MOUSE, it becomes clear that these are very different proteins. They are part of the same family because of two shared matches, LIGDAAK and IINEPTAAAIAYGLD, but many highly significant matches would have to be discarded for either protein to become a sub-set of the other. In this way, we can quickly deduce from the Protein Family Summary that there is abundant evidence that both BIP_MOUSE and HSP7C_MOUSE were present in the sample. There is little evidence for HS71L_MOUSE. It is more likely that the HSP7C_MOUSE contained a SNP or two relative to the database sequence.

The peptide match table contains the following columns:

1. Query number, hyperlinked to Peptide View.
2. Dupes is a count of the number of additional matches to the same peptide sequence with the same modifications and charge. Click on the triangle link to expand these duplicate matches, which will have the same or lower score than the one first listed
3. Experimental m/z value
4. Experimental m/z transformed to a relative molecular mass
5. Relative molecular mass calculated from the matched peptide sequence
6. Difference (error) between the experimental and calculated masses
7. Number of missed cleavage sites
8. Ions score – If there are duplicate matches to the same peptide, then the lower scoring matches are shown in brackets.
9. Expectation value for the peptide match. (The number of times we would expect to obtain an equal or higher score, purely by chance. The lower this value, the more significant the result).
10. Rank of the peptide match, (1 to 10, where 1 is the best match). If there is a triangle to the left of the rank, the row can be expanded to show the alternative matches for this query.
11. A letter U if the peptide sequence is unique to one protein family member.
12. A column is displayed for each family member selected by its checkbox immediately above the table. A marker is shown if the peptide match is present in the protein. Where a column represents more than one protein, and the peptide is found in some of these proteins, but not all, the marker is grey. Otherwise, it is black.
13. Sequence of the peptide in 1-letter code. The residues that bracket the peptide sequence in the protein are also shown, delimited by periods. If the peptide forms the protein terminus, then a dash is shown instead.
14. Any variable modifications used to obtain the match

If the peptide sequence is modified, each affected residue is underlined. Details of the modification will be displayed if the mouse cursor is rested over the residue. If multiple matches to a query have identical scores, i.e. the sequences are different, but are identical in mass spectrometry terms, they are collapsed into a single consensus peptide sequence for display. The residues that differ between the matches are displayed in lower case. For example, if deamidation was a variable modification and one protein contained the sequence FASFIDK and another protein in the same family contained FASFINK (deamidation at N) then the table would display FASFIdK. Click on the rank to expand the alternative matches for the query and the actual peptide sequences will be displayed.

Controls at the top and bottom of the tab can be used to move between pages and change the number of protein families per page. There are also buttons to expand and collapse all of the information on the page.

At the top of the tab, there are text search controls. You can search the report for proteins and peptides containing numerical or text values.

Search for proteins by:

• Accession
• Description
• Family number
• Page number

Search for peptides by:

• Query number
• Observed m/z
• Mr(expt)
• Mr(calc)
• Sequence
• Fixed modification
• Variable modification

If the target is found, the first occurrence will be highlighted and, if necessary, the page will scroll and expand. If the target is found in multiple locations in a single family, all matches will be highlighted. Choose Next or Previous to jump forward or backward to other instances of the target in other families. If the target is not found, a button provides the option to try the search in the Unassigned tab.

Report Builder

The Report Builder tab allows you to build a customised table of protein hits, which is particularly useful if you need a minimal list of proteins for a publication. You can choose which columns to include and their order, filter out proteins that are of no interest, such as one-hit wonders, and export the table in CSV format directly to Excel.

The table has one row for each of the top-level protein hits, sometimes called anchor proteins. Since a family can contain several family members, grouped because they have shared peptides, there will be as many rows in the table as there are family members in the report. If the search results contain same-set proteins, and a preferred taxonomy has been selected, this will also apply to the selection of anchor proteins for the table. You can sort the table by clicking on a column header. The currently active sort order is shown by an arrow in the relevant column; up means ascending, down means descending. The table can be exported as CSV with one click, with sort order preserved.

The columns are mostly self-explanatory, and tooltip help is displayed when the mouse pointer rests over a column header. Clicking on a family number hyperlink will jump to the family displayed in the proteins tab. Clicking on an accession hyperlink will load a Protein View report. If the search included quantitation using Reporter or Multiplex protocols, protein level quantitation information is also available. To select and re-order columns, expand the Columns section.

Use the Arrangement drop down list to load a saved arrangement or choose <custom> to configure the report by moving columns between the two lists. The columns are categorised into groups. The basic set of columns that are always available are under “Protein hits”. Quantitation results create a set of columns for each reported ratio. In the enabled list, you can select individual columns, CTRL+click multiple columns, or SHIFT+click a range of columns and use the up and down arrows to change their relative position. The changes take effect when you choose Apply.

If Mascot security is enabled and there is an arrangement you might want to use again, you can save the arrangement in your security session. After choosing Apply, give the arrangement a name and choose Save. Saved arrangements can be loaded using the drop down list mentioned earlier. If you want the arrangement to be available to all users, choose ‘Show column string’, copy the text, and use it to create an additional ReportBuilderColumnArrangement_N entry in mascot.dat.

The Filters section enables protein rows to be dropped according to multiple criteria. Configure the first term and apply it by choosing Filter. The table will be reloaded and additional controls displayed to allow another term to be added, if required. Often, a single term requiring each protein to have significant matches to at least two distinct sequences will be all that is needed. On the other hand, for a quantitation report, it is might be very useful to create a table such as this, limited to proteins that are significantly up-regulated in the 117 channel and significantly down-regulated in the 116 channel.

Unassigned Peptide Matches

The unassigned list contains peptide matches that are not assigned to protein families. In some cases, there may be no match at all, and only the observed m/z value and the experimental Mr will be listed against the query number. In other cases, details of the top scoring peptide match will be listed.

The list is split into pages. Controls at the top and bottom of the tab can be used to move between pages and change the number of matches per page. The Sort unassigned control allows the sort order to be changed. Descending score makes it easy to see whether there are any good matches. If so, you will want to increase the number of protein families or set it to AUTO so as to pull these matches into the main body of the report. Ascending query number is the same as ascending precursor Mr. Descending intensity allows you to find spectra with intense peaks that have failed to get a match. These could be candidates for de novo sequencing.

The unassigned table contains the following columns:

1. Query number, hyperlinked to Peptide View.
2. Experimental m/z value
3. Experimental m/z transformed to a relative molecular mass
4. Relative molecular mass calculated from the matched peptide sequence
5. Difference (error) between the experimental and calculated masses
6. Number of missed cleavage sites
7. Ions score
8. Expectation value for the peptide match. (The number of times we would expect to obtain an equal or higher score, purely by chance. The lower this value, the more significant the result).
9. Rank of the peptide match, (1 to 10, where 1 is the best match). This will always be 1 for matches in the unassigned list. If there is a triangle to the left of the rank, the row can be expanded to show the alternative matches for this query
10. Sequence of the peptide in 1-letter code with modified residues underlined.
11. Any variable modifications used to obtain the match

When you load the peptide view for an unassigned query, it takes the first protein containing the matched peptide. This may or may not be the protein that would be selected as the anchor protein if the formatting was changed in a way that caused the match to be pulled into a family in the Proteins tab.

At the top of the tab, there are text search controls. You can search the unassigned list by query number, mass, m/z value, and peptide sequence. Select the category, enter text in the edit field and choose Filter. If the text is found, the complete unassigned list is filtered to display matching queries. Choose Clear to return to the standard display. If the text is not found, a button provides the option to try the search in the Proteins tab.

Peptide Summary

Sections of the report are described in the order in which they appear. Use this link to open an example report in a new browser window or tab.

Header

At the top of the report are a few lines to identify the search uniquely: search title, date, user name, etc. The database version is identified with either a release number or an ISO datestamp. The accessions and descriptions for the top scoring protein hits are listed.

If the search included the auto-decoy option, false discovery rate information is displayed at this location.

Score Distribution

Following the header, a histogram illustrates the protein score distribution. The 50 highest protein scores are divided into 16 bins according to their score, and the heights of the bars show the number of matches in each bin.

For a search of MS/MS data, protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. The protein score histogram has little meaning for MS/MS results, but is retained for historical reasons. The green shaded area extends up to the average identity threshold for an individual peptide match.

Format Controls

These controls enable the report format to be modified. After making changes, press the "Format As" button to reload the report using the new settings.

• Report format Choose from the list of available formats
• Significance threshold The default significance threshold is p < 0.05. You can change this to any value in the range 0.99 to 1E-18.
• Maximum number of hits This value was initially chosen when the search was submitted. Enter a positive integer if you wish to re-specify the number of protein hits to report. Of course, the total number of hits actually found by the search may be less. Entering the word AUTO or a value of 0 will display all of the hits that have a protein score exceeding the average identity threshold score for an individual peptide match.
• Standard or MudPIT scoring MudPIT scoring is a more aggressive protein score that removes protein hits that have high protein scores purely because they have a large number of low-scoring peptide matches. It is the default protein score for a search in which the ratio of the number of queries to the number of entries in the database, (after any taxonomy filter), exceeds 0.001.
• Ions score cut-off Values greater than 0 and less than 1 act as an expect value threshold, and the scores for any peptide matches with higher expect values are suppressed. Values of 1 or more act as a score threshold, and any peptide matches with lower scores are suppressed. By setting this to (say) 20, you cut out all of the very low scoring, random peptide matches. This means that homologous proteins are more likely to collapse into a single hit.
• Show sub-sets By default, each hit in a Peptide Summary shows the set of proteins that match a particular set of peptides. Proteins that match a sub-set of those peptides are not shown. You can choose to show these additional protein hits, but be aware that this can make the report very much longer. To show all sub-set proteins, set Show sub-sets to 1. To show no sub-set proteins, set it to 0. Intermediate values set a threshold on the difference in protein score between the primary hit and the sub-set hit expressed as a fraction. For example, if the protein score of the primary hit was 400, and Show sub-sets was 0.75, sub-set hits with scores of 100 or more would be displayed.
• Show or Suppress pop-ups The JavaScript pop-up windows, that show the top 10 peptide matches for each query, are very useful, but they make the HTML report larger and slower to load in a web browser. If you have a report that never seems to load, or is very slow to scroll, try suppressing the pop-ups.
• Sort unassigned These are sorting options for the list of peptide matches that are not assigned to protein hits. Descending score makes it easy to see whether there are any good matches. If so, you will want to increase the number of protein hits or set it to AUTO so as to pull these matches into the main body of the report. Ascending query number is the same as ascending precursor Mr. Descending intensity allows you to find strong spectra that have failed to get a match. These could be candidates for de novo sequencing.
• Require bold red Requiring a protein hit to include at least one bold red peptide match is a good way to remove duplicate homologous proteins from a report. See the discussion in Results Interpretation for further information.

The following controls are only displayed for certain types of search:

• UniGene index (Only displayed for a search of a nucleic acid database when UniGene index files have been configured) Choose the UniGene index to be used to cluster the protein hits into gene based families.
• Hide error tolerant matches (Only displayed for an automatic error tolerant search) Check to hide the additional, error tolerant matches.
• Show Percolator scores (Only displayed for searches that satisfy the requirements for using Percolator) Check to display scores and expect values adjusted by Percolator.

If the search used a quantitation method specifying Multiplex or Reporter protocol, there will be an additional block of quantitation related controls, as described here.

Repeating a search

A search can easily be repeated, so as to investigate the effect of changes in search parameters. Queries can selected in the result report, then loaded into a search form, where the search parameters can be modified.

Checkboxes for selecting queries for a repeat search are included in the body of the report, wherever the top rank match fir a particular query first appears. You can toggle individual checkboxes or use the Select All and Select None buttons to change the states of all checkboxes. Search Selected invokes the search form.

There is a second series of checkboxes, one for each protein hit, that have a dual purpose. If you wish to perform a manual error tolerant search, first check the Error Tolerant checkbox then select the proteins to be searched in the second pass search. Press Search Selected to invoke the search form.

If the Error Tolerant checkbox is not checked, the checkboxes select protein hits for an Archive Report

Protein Hit List

The body of the Peptide Summary report contains a tabular listing of the proteins, sorted by descending protein score. For each protein, the first line contains the accession string, (linked to the corresponding Protein View), the protein molecular mass, and the protein score. The number of queries matched to the protein completes the first line. The second line is the protein description taken from the Fasta entry. This is followed by a table summarising the matched peptide masses. The table columns contain:

1. Checkboxes for selecting queries for a repeat search will appear in the first column of any row containing the first appearance of a top ranked match.
2. Query number, hyperlinked to Peptide View.
3. Experimental m/z value
4. Experimental m/z transformed to a relative molecular mass
5. Relative molecular mass calculated from the matched peptide sequence
6. Difference (error) between the experimental and calculated masses
7. Number of missed cleavage sites
8. Ions score – If there are duplicate matches to the same peptide, then the lower scoring matches are shown in brackets.
9. Expectation value for the peptide match. (The number of times we would expect to obtain an equal or higher score, purely by chance. The lower this value, the more significant the result).
10. Rank of the ions match, (1 to 10, where 1 is the best match).
11. A letter U if the peptide sequence is unique to the protein hit
12. Sequence of the peptide in 1-letter code. The residues that bracket the peptide sequence in the protein are also shown, delimited by periods. If the peptide forms the protein terminus, then a dash is shown instead.
13. Any variable modifications found in the peptide

If the search used a quantitation method specifying Multiplex or Reporter protocol, there will be an additional rows and columns of quantitation information, as described here.

An abbreviated listing follows for any proteins that contain the same set of peptide matches. It is also possible to display proteins containing a sub-set of peptide matches, but this is disabled by default. It can be enabled globally in the configuration file, mascot.dat, or enabled for a single report by using the checkbox in the format controls.

Yellow Pop-up

Clicking on the query number link opens the Peptide View for the match in a new browser window or tab. Resting the mouse cursor over the query number link causes a pop-up window to appear, displaying the complete list of peptide matches for that query. The pop-up window displays the query title (if any) followed by one or two significance thresholds, which are described in detail here. Below this, a table containing information on the highest scoring peptide matches for the query:

1. Ions score
2. Expect value
3. Difference (error) between the experimental and calculated masses
4. Hit number of the (first) protein containing the peptide match. A plus sign indicates that multiple proteins contain a match to this peptide
5. Accession string of the (first) protein containing the peptide match.
6. Sequence of the peptide in 1-letter code. If a variable modification has been used to obtain a match, the modified residue is underlined. If the residues that bracket the peptide sequence are the same in all the proteins that contain it, then these residues are also shown, delimited by periods. If the peptide forms the protein terminus, then a dash is shown instead.

Unassigned Peptide Matches

The unassigned list contains peptide matches that are not assigned to proteins in the body of the report. In some cases, there may be no match at all, and only the observed m/z value and the experimental Mr will be listed. In other cases, the top scoring peptide match will be listed.

So, unassigned doesn’t necessarily mean unmatched or not significant. Its the overflow, if you like. If you reformat the report, asking for more and more protein hits, all of the unassigned matches with non-zero scores would eventually get pulled into the body of the report.

When you load the peptide view for an unassigned query, it takes the first protein containing the matched peptide. This may or may not be the protein that would be selected as the primary hit if the peptide match was pulled into the body of the report.

Search Parameters

At the foot of the report, the search parameters are summarised. Descriptions of individual search parameters can be found here.

Select Summary

Use this link to open an example report in a new browser window or tab.

The Select Summary was inspired by David Tabb’s DTASelect. It is very similar to the Peptide Summary, but more compact because multiple matches to the same peptide sequence are collapsed into a single line. Also, the list of peptide matches that are not assigned to any protein hit is split off into a separate report.

The differences between the Select Summary and the Peptide Summary are as follows:

1. The Search Parameters are moved up into the header
2. There is no Score Distribution histogram
3. There are no checkboxes against protein hits or peptide matches. The choices for repeating a search are set by radio buttons for All queries, Unassigned, Below homology threshold, and Below identity threshold. This means that you cannot use a Select Summary for a manual error tolerant search or to create an Archive Report
4. In the Protein Hit List, if multiple queries match to the same peptide (the same sequence, modifications and charge state) full details are displayed for the highest scoring match only. Any matches with lower scores are listed as additional query number links after the peptide sequence.
5. Variable modifications are not listed after the peptide sequence, but are indicated by underlined residues.
6. Unassigned Peptide Matches are split off into a separate report. Use the format controls to display this report.

Archive Report

Use this link to open an example report in a new browser window or tab.

An Archive Report is a Peptide Summary in which only selected protein hits appear. There is no unassigned list and no controls for changing the format or repeating the search. You might use this format to give a colleague a list of validated protein hits, or to remove hits that are contaminants or of no interest, etc.