Results: 4

1.
Fig. 2.

Fig. 2. From: Shotgun Protein Sequencing with Meta-contig Assembly.

Annotation of contigs and meta-contigs with MS-GFDB spectrum identifications. The annotation of a SPS contig is shown here but the same procedure applies for meta-contigs. Above the contig PRM spectrum are all sequence calls that align to the reference. Below the contig PRM spectrum are all spectra from overlapping peptides that were assembled to yield the contig PRM spectrum. Only assembled peaks are shown in each assembled PRM spectrum. For a sequence call to be labeled correct, it must be flanked by at least one pair of annotated PRM or SRM peaks in the same ion series that map to the same protein. If a sequence call that is not labeled correct is flanked by at least one pair of peaks from an identified spectrum then it is labeled incorrect. If a sequence call is not flanked by at least one pair of peaks from an identified spectrum then it is labeled un-annotated.

Adrian Guthals, et al. Mol Cell Proteomics. 2012 October;11(10):1084-1096.
2.
Fig. 4.

Fig. 4. From: Shotgun Protein Sequencing with Meta-contig Assembly.

Mapped Meta-contigs. Meta-contig PRM spectra were aligned to reference proteins to evaluate de novo sequencing coverage. Every colored row corresponds to a contig PRM spectrum as separately mapped to the target protein sequence (information not used by Meta-SPS). Every set of overlapping contigs of the same color corresponds to a meta-contig; sets of contigs of the same color with no overlap indicate separate meta-contigs. Below each coverage map is the longest meta-contig sequence of the boxed meta-contig for the corresponding protein. Purple gaps correspond to mapped sequence calls with PTMs verified by MS-GFDB; blue gaps correspond to mapped gaps that span 2 or more residues in the reference. Remaining un-colored residues represent sequence calls that map to reference amino acid masses. A, Meta-contig coverage of kallikrein-related peptidase from the 6-prot sample is displayed here; 8 meta-contigs covered 78% of the 261 AA protein with the longest sequence spanning 94 AA. B, Meta-contig coverage of the aBTLA light chain is displayed here; 9 meta-contigs covered 87% of the 219 AA protein with the longest sequence spanning 107 AA.

Adrian Guthals, et al. Mol Cell Proteomics. 2012 October;11(10):1084-1096.
3.
Fig. 1.

Fig. 1. From: Shotgun Protein Sequencing with Meta-contig Assembly.

Meta-SPS Procedures. A, Green arrows denote procedures previously described in (1) and red arrows denote procedures described here. The SPS step involves spectral clustering by MSCluster (34), PepNovo+ PRM scoring (35), and assembly of mass spectra into contigs (1). B, An alignment between two PRM spectra is represented as the shift of the second spectrum wrt the first that yields the highest possible score. The displayed scoring function takes the minimum matched/overlapping intensity ratio and multiplies by the number of matching peaks (denoted by MP(A) for alignment ASi,Sj〉 between contig PRM spectra Si and Sj). Matched and overlapping intensities for each spectrum are displayed as red and blue boxed regions, respectively. Sequences are not known in advance; shown only for illustration purposes. C, Here aligned SPS contigs are assembled into meta-contigs by iteratively merging the highest scoring alignment until remaining alignments have a low score. By merging the highest scoring alignment at every iteration, it is guaranteed that all inconsistent alignments that were removed have a lower score. D, Green arrows denote merged alignments and numbers correspond to the order in which they alignments are merged. Initially, every contig was in its own meta-contig. The 6 meta-contigs were then merged by five alignments, yielding a single meta-contig PRM spectrum and its meta-contig sequence.

Adrian Guthals, et al. Mol Cell Proteomics. 2012 October;11(10):1084-1096.
4.
Fig. 3.

Fig. 3. From: Shotgun Protein Sequencing with Meta-contig Assembly.

De novo sequencing length, coverage, and accuracy. A, The x axis plots the minimum distance (k) a sequence call or gap is from one end of a meta-contig sequence and the y axis plots the average sequencing accuracy over all annotated calls at each k-distance. Over all annotated calls reported more than 8 positions from their closest end, there were a total of 3 incorrect sequence calls at k = 20, 21, and 22 of a single meta-contig aligned to the aBTLA heavy chain (discussed in the Results section of Supplementary Materials). B, Protein identifiers are: P1 - leptin precursor, P2 - kallikrein-related peptidase, P3 - GroEL, P4 - myoglobin, P5 - aprotinin, P6 - peroxidase, P7 - aBTLA light chain, and P8 - aBTLA heavy chain. Protein Length is the length of each reference protein in amino acid residues. Spectrum Coverage is the percent of each protein covered by peptides identified MS-GFDB with 1% FDR. Coverage is taken over all mapped contigs and Accuracy is taken over all identified meta-contigs. Mapped meta-contigs must be aligned to a reference protein as described in the text whereas identified meta-contigs must assemble at least one identified spectrum whose peptide sequence is a substring of a reference protein. Sequencing Coverage is the percent of amino acids in each protein covered by at least one mapped meta-contig sequence. Coverage Redundancy is the average number of mapped meta-contig sequences covering each amino acid residue that is covered by at least one meta-contig sequence. Spectra Per Meta-contig is the average number of spectra assembled by each mapped meta-contig whereas Peptides Per Meta-contig is the average number of peptides (spectra with distinct parent masses) assembled by each mapped meta-contig. Average Seq. Length is the average number of amino acid residues covered by each mapped meta-contig and Longest Sequence is the maximum number of amino acid residues covered by a mapped meta-contig. Correct Sequence Calls is the percentage of annotated sequence calls that were correct in identified meta-contigs. Un-annotated Seq. Calls is the percentage of sequence calls that were un-annotated in identified meta-contigs.

Adrian Guthals, et al. Mol Cell Proteomics. 2012 October;11(10):1084-1096.

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