PEAKS: SPIDER (Sequence Homology Search Tool)

SPIDER is used to reconstruct sequences as well as improve coverage on proteins already in a database. This is accomplished by seeking exact sequence matches and plugging these sequences into a specialized database. This substitution occurs using one of three highly acclaimed methods: Segment Match, Non-Gapped Homology Match and Homology Match.

Segment Match: this is not a true mutation search, instead, it will insist that the mass of the peptide returned is the same as that of the de novo sequence. Supports fixed modifications.

Non-gapped Homology Match: this search will allow for transpositions, and single point mutations but not insertions or deletions. Supports fixed modifications.

Homology (Block) Match: this is the most rigorous and most resource intensive search mode, taking into account all types of mutations and positional confidence scores. A quick version of this is used to create the reconstructed peptides and to generate the final scores in each of the previous search modes. Also, with this method users can define variable modifications as well as fixed modifications.

Additional capabilities to note about SPIDER include amino acid selection, mass tolerance and number of peptides to report. Regarding the amino acid selection this means if you would like SPIDER to treat Leucine equal to Isoleucine without a penalty in the score, this is certainly possible. Additionally, it is posssible to treat Lysine equal to Glutamine without penalty.

SPIDER will search the database for homologous peptides and attempt to consolidate these into protein hits as well. The result report will look very similar to the results for PEAKS Protein ID or inChorus searching.

The Peptide View displays results that look very much like the results for PEAKS Protein ID. Within this pane resides the Peptide details which display the SPIDER matches shown in red.

When simply identifying exact peptides from the database, using PEAKS Protein ID, or inChorus, there�s no need to reconstruct the �real� sequence.

In addition to peptides, SPIDER offers a Protein View which yields a similar display to PEAKS Protein ID. This time, instead of homologus (blue) regions, there are now red regions to indicate areas of mutation found by SPIDER.

Sequence Browser

The specific sequence(s) noted in red are more clearly visible here in the Sequence Browser.

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Overview De Novo Sequencing Database Search Multiple Database Search Sequence Homology PTM Quantification RAW Data Tech Support Our Research User Comments User Research Download Demo Request Prices	Superior de novo sequencing and protein ID Software PEAKS SPIDER Expanded SPIDER is used to reconstruct sequences as well as improve coverage on proteins already in a database. This is accomplished by seeking exact sequence matches and plugging these sequences into a specialized database. This substitution occurs using one of three highly acclaimed methods: Segment Match, Non-Gapped Homology Match and Homology Match. Click image to view full scale SPIDER Search Options window Segment Match: this is not a true mutation search, instead, it will insist that the mass of the peptide returned is the same as that of the de novo sequence. Supports fixed modifications. Non-gapped Homology Match: this search will allow for transpositions, and single point mutations but not insertions or deletions. Supports fixed modifications. Homology (Block) Match: this is the most rigorous and most resource intensive search mode, taking into account all types of mutations and positional confidence scores. A quick version of this is used to create the reconstructed peptides and to generate the final scores in each of the previous search modes. Also, with this method users can define variable modifications as well as fixed modifications. Additional capabilities to note about SPIDER include amino acid selection, mass tolerance and number of peptides to report. Regarding the amino acid selection this means if you would like SPIDER to treat Leucine equal to Isoleucine without a penalty in the score, this is certainly possible. Additionally, it is posssible to treat Lysine equal to Glutamine without penalty. Peptide Details Click image to view full scale SPIDER Peptide Details View SPIDER will search the database for homologous peptides and attempt to consolidate these into protein hits as well. The result report will look very similar to the results for PEAKS Protein ID or inChorus searching. The Peptide View displays results that look very much like the results for PEAKS Protein ID. Within this pane resides the Peptide details which display the SPIDER matches shown in red. Letters on a green background and with vertical bars, indicate agreement. Letters on a red background indicate sequencing error. Color codes on the de novo sequence letters still indicate positional confidence. Letters on a blue background indicate uncertainty or mutation. When simply identifying exact peptides from the database, using PEAKS Protein ID, or inChorus, there�s no need to reconstruct the �real� sequence. Protein View Click image to view full scale SPIDER Protein View In addition to peptides, SPIDER offers a Protein View which yields a similar display to PEAKS Protein ID. This time, instead of homologus (blue) regions, there are now red regions to indicate areas of mutation found by SPIDER. Sequence Browser Click image to view full scale SPIDER Sequence Browser The specific sequence(s) noted in red are more clearly visible here in the Sequence Browser.