| Sample: | | |
|---|---|---|
| Project code | DAVID_chicken_soluble | DAVID_chicken_insoluble |
| Species | Gallus gallus | Gallus gallus |
| Cell Type | eye lens fiber cells | eye lens fiber cells |
| Mass Spec: | | |
| Instrument | Thermo Orbitrap Fusion | Thermo Orbitrap Fusion |
| LC System | Thermo Unitimate 3000 | Thermo Unitimate 3000 |
| LC Duration (min) | 120 | 120 |
| Capillary Temperature (degree C) | 275 | 275 |
| Ion Source | Thermo Easy-Spray | Thermo Easy-Spray |
| Source potential | 2.4 kV | 2.4 kV |
| Lock mass | yes (user defined mass) | yes (user defined mass) |
| Full m/z range (Th) | 400 - 1600 | 400 - 1600 |
| Full Resolution | 120,000 | 120,000 |
| Full AGC Target | 400,000 | 400,000 |
| Full Maximum Inject Time (millisec) | 50 | 50 |
| Number of dependent MS2 scans | Top N, 3 sec cycle | Top N, 3 sec cycle |
| MS2 collision type | HCD | HCD |
| MS2 AGC | 10,000 | 10,000 |
| MS2 Maximum Inject Time (millisec) | 35 | 35 |
| Isolation Window (th) | 2 | 2 |
| Minimum Ion intensity | 50,000 | 50,000 |
| Normalized Collision Energy | 30 | 30 |
| MS2 m/z range (Th) | 120 - 2000 | 120 - 2000 |
| Rejeced Charge States | 1+ and greater than 7+ | 1+ and greater than 7+ |
| MIPS filter | on | on |
| Exclusion Repeat Count | 1 | 1 |
| Exclusion mass low (PPM) | 10 | 10 |
| Exclusion mass high (PPM) | 10 | 10 |
| Exclusion List size | 500? | 500? |
| Exclusion Duration (second) | 30 30 | |
| FASTA protein database: | | |
| Database source | UniProt (proteome_UP000000539) | UniProt (proteome_UP000000539) |
| Download date | 12-Dec-14 | 12-Dec-14 |
| Number of protein sequences | 17,623 | 17,623 |
| Include common contaminants | yes (179 sequences) | yes (179 sequences) |
| Decoy sequence type | reversed | reversed |
| Database preparation software | ||
| Peak list creation: | | |
| MSConvert version | 3.0.6618 | 3.0.6618 |
| Minimum ion count | 15 | 15 |
| Minimum intensity (absolute) | 100 | 100 |
| MSn level | 2 | 2 |
| Number of MS2 scans | 64,121 | 101,530 |
| Search engine: | | |
| Comet version | 2014.02 rev. 2 | 2014.02 rev. 2 |
| Database | uniprot-proteome_UP000000539_chick_both.fasta | uniprot-proteome_UP000000539_chick_both.fasta |
| Parent ion mass tolerance | 1.25 | 1.25 |
| Parent ion mass type | monoisotopic | monoisotopic |
| Search enzyme | trypsin strict (KR not if P) | trypsin strict (KR not if P) |
| Fully tryptic termini | yes | yes |
| Maximum missed cleavages | 2 | 2 |
| Variable modifications | M+15.9949 | M+15.9949 |
| Maximum number of variable mods per peptide | 3 | 3 |
| Fargment ion tolerance | 1.0005 | 1.0005 |
| Fragment ion bin offset | 0.4 | 0.4 |
| Fragment ion mass type | monoisotopic | monoisotopic |
| Ion series used in scoring | y, b, NL | y, b, NL |
| Maximum parent ion charge state | 4 | 4 |
| Maximum fragment ion charge state | 3 | 3 |
| Theoretical digest mass range | 600 - 5000 | 600 - 5000 |
| Static modifications | C+57.0215 | C+57.0215 |
| Peptide to protein mapping: | | |
| Software | PAW pipeline (in-house) | PAW pipeline (in-house) |
| Number scans passing score thresholds | 29,913 | 47,308 |
| Number decoys passing score thresholds | 369 | 560 |
| PSM FDR (scan-based) | 1.20% | 1.20% |
| Parsimony analysis | basic subset removal | basic subset removal |
| Minimum peptides per protein | 2 | 2 |
| Minimum unique peptides per protein | 0 | 0 |
| Number of identified proteins (non-redundant, without grouping) | 1078 (39 contaminants) | 1759 (54 contaminants) |
| Number of decoy proteins (non-redundant, without grouping) | 6 | 12 |
| Preliminary protein FDR | 0.60% | 0.50% |
| Protein grouping method | extended parsimony (in-house software) | extended parsimony (in-house software) |
| Header | Description |
|---|---|
| ProtGroup | arbitrary protein group number (groups have more than one member for redundant proteins or homologous families) |
| Counter | column used to count visible rows in results files using Excel |
| Accession | protein database accession string |
| Identical | accessions of all redundant proteins (indistinguishable peptide sets) |
| Similar | accessions of all proteins having sufficiently similar peptide sets (homologous families) |
| OtherLoci | list of all protein accessions having any shared peptides in common with respective protein |
| Link | hyperlink Excel function to UniProt protein database |
| Filter | text column for flagging contaminants, decoys, etc. |
| Sort | column for controlling row order |
| Coverage | protein sequence coverage in % |
| SeqLength | number of amino acids in protein database entry |
| MW | calculated molecular weight (average mass in Da) for protein database entry |
| Description | protein database description string |
| Gene | UniProt gene name |
| CountsTot | grand total of all intensities (shared and unique) across all N samples |
| UniqueTot | grand total of all unique intensities across all N samples |
| UniqFrac | ratio of UniqueTot to CountsTot (small fractions indicate many shared peptides) |
| DAVID_chicken_in_20141201 | total peptide intensities for water-insoluble fraction |
| DAVID_chicken_sol_20141202 | total peptide intensities for water-insoluble fraction |
| DAVID_chicken_insol_20141201 | total unique peptide intensities for water-insoluble fraction |
| DAVID_chicken_sol_20141202 | total unique peptide intensities for water-insoluble fraction |
| DAVID_chicken_insol_20141201 | total corrected peptide intensities for water-insoluble fraction (shared peptide intensities fractionally split based on relative unique intensities) |
| DAVID_chicken_sol_20141202 | total corrected peptide intensities for water-insoluble fraction (shared peptide intensities fractionally split based on relative unique intensities) |
| AccessionClean | used to lookup Ensembl information |
| query_acc | full UniProt accession key (accession, identifier, and database source) |
| query_desc | full UniProt protein description string |
| hit_acc | Ensembl database accession |
| hit_desc | Ensembl database description |
| blast_scores | BLAST alignment scores between UniProt and Ensembl best matches |
| status | BLAST alignment status (OK, partial matches, or no match) |
| Header | Description |
|---|---|
| ProtGroup | arbitrary protein group number (groups have more than one member for redundant proteins or homologous families) |
| Counter | column used to count visible rows in results files using Excel |
| Accession | protein database accession string |
| Identical | accessions of all redundant proteins (indistinguishable peptide sets) |
| Similar | accessions of all proteins having sufficiently similar peptide sets (homologous families) |
| OtherLoci | list of all protein accessions having any shared peptides in common with respective protein |
| Link | not used |
| Filter | text column for flagging contaminants, decoys, etc. |
| Coverage | protein sequence coverage in % |
| SeqLength | number of amino acids in protein database entry |
| MW | calculated molecular weight (average mass in Da) for protein database entry |
| Description | protein database description string |
| Gene | UniProt gene name |
| CountsTot | grand total of all counts (shared and unique) across all N samples |
| UniqueTot | grand total of all unique counts across all N samples |
| UniqFrac | ratio of UniqueTot to CountsTot (small fractions indicate many shared peptides) |
| DAVID_chicken_insol_20141201 | total peptide counts for water-insoluble fraction |
| DAVID_chicken_sol_20141202 | total peptide counts for water-insoluble fraction |
| DAVID_chicken_insol_20141201 | total unique peptide counts for water-insoluble fraction |
| DAVID_chicken_sol_20141202 | total unique peptide counts for water-insoluble fraction |
| DAVID_chicken_insol_20141201 | total corrected peptide counts for water-insoluble fraction (shared peptide counts fractionally split based on relative unique counts) |
| DAVID_chicken_sol_20141202 | total corrected peptide counts for water-insoluble fraction (shared peptide counts fractionally split based on relative unique counts) |
| Header | Description |
|---|---|
| ProtGroup | arbitrary protein group number (groups have more than one member for redundant proteins or homologous families). Cross references with protein reports. |
| Accession | protein database accession string |
| Sequence | peptide sequence (M* denotes oxidized Met) |
| Begin | beginning amino acid residue number |
| End | ending amino acid number |
| Unique | indicates whether peptide is matched to a single proptein or not |
| NTT | number of peptide termini consistent with tryptic cleavage |
| Z | peptide charge state |
| TotCount | total number of MS2 spectra mapped to peptide in the respective charge state |
| DAVID_chicken_insol_20141201 | total count in the insoluble fraction |
| DAVID_chicken_sol_20141202 | total count in the soluble fraction |
| OtherLoci | list of all protein accessions having any shared peptides in common with respective protein |
| Header | Description |
|---|---|
| ProtGroup | arbitrary protein group number (groups have more than one member for redundant proteins or homologous families). Cross references with protein reports. |
| Accession | protein database accession string |
| Sequence | peptide sequence (M* denotes oxidized Met) |
| Unique | indicates whether peptide is matched to a single proptein or not |
| TotCount | total number of MS2 spectra mapped to peptide in the respective charge state |
| NTT | number of peptide termini consistent with tryptic cleavage |
| XCorr | SEQUEST score for the top-scoring match to this peptide sequence |
| DeltaCN | delta XCorr score for the top-scoring match to this peptide sequence |
| SpRank | preliminary scoring rank for the top scoring match to this peptide |
| NewDisc | discrimiant function score for the top scoring match to this peptide |
| Z | peptide charge state |
| Delta_Mass | difference between experimental and calculated masses for the top scoring match to this peptide |
| Exp_Mass | experimentally measured mass for the top scoring match to this peptide |
| Calc_Mass | calculated mass for this peptide sequence |
| DTA_filename | the equivalent DTA name for the top scoring match to this peptide |
| Header | Description |
|---|---|
| ProtGroup | arbitrary protein group number (groups have more than one member for redundant proteins or homologous families). Cross references with protein reports. |
| Accession | protein database accession string |
| Sequence | peptide sequence (M* denotes oxidized Met) |
| Unique | indicates whether peptide is matched to a single proptein or not |
| TotCount | total number of MS2 spectra mapped to peptide in the respective charge state |
| NTT | number of peptide termini consistent with tryptic cleavage |
| XCorr | SEQUEST score for the top-scoring match to this peptide sequence |
| DeltaCN | delta XCorr score for the top-scoring match to this peptide sequence |
| SpRank | preliminary scoring rank for the top scoring match to this peptide |
| NewDisc | discrimiant function score for the top scoring match to this peptide |
| Z | peptide charge state |
| Delta_Mass | difference between experimental and calculated masses for the top scoring match to this peptide |
| Exp_Mass | experimentally measured mass for the top scoring match to this peptide |
| Calc_Mass | calculated mass for this peptide sequence |
| DTA_filename | the equivalent DTA name for the top scoring match to this peptide |
| Header | Description |
|---|---|
| Ident | UniProt identifier (lookup key) |
| query_number | arbitrary query number during BLAST run |
| query_acc | UniProt accession |
| query_desc | UniProt description string |
| hit_acc | Ensembl accession for top BLAST match |
| hit_desc | Ensembl description string for top BLAST match |
| blast_scores | a composite string with various BLAST match scores |
| status | text column designating quality of BLAST match based on set of matches |
| Acc | UniProt stable accession key |
| Ident | UniProt more informative identifier key |
| Header | Description |
|---|---|
| Accession | protein database accession string |
| Coverage | protein sequence coverage in % |
| Length | number of amino acids in protein database entry |
| UniProt Description | UniProt protein database accession string |
| Ensembl Description | Ensembl protein database accession string |
| Gene | UniProt gene name |
| Water-Insoluble (intensities) | water-insoluble lens fraction (raw intensities) |
| Water-Soluble (intensities) | water-soluble lens fraction (raw intensities) |
| Water-Insoluble (relative abundances) | water-insoluble lens fraction (relative crystallin abundances using raw intensities) |
| Water-Soluble (relative abundances) | water-soluble lens fraction (relative crystallin abundances using raw intensities) |
| Water-Insoluble (length normalized) | water-insoluble lens fraction (raw intensities normalized by sequence length) |
| Water-Soluble (length normalized) | water-soluble lens fraction (raw intensities normalized by sequence length) |
| Water-Insoluble (relative abundances) | water-insoluble lens fraction (relative crystallin abundances using raw intensities normalized by sequence length) |
| Water-Soluble (relative abundances) | water-soluble lens fraction (relative crystallin abundances using raw intensities normalized by sequence length) |