High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

  1. Allyson Li
  2. Rashmi Voleti
  3. Minhee Lee
  4. Dejan Gagoski
  5. Neel H Shah  Is a corresponding author
  1. Department of Chemistry, Columbia University, United States
  2. Department of Biological Sciences, Columbia University, United States
11 figures, 2 tables and 1 additional file

Figures

Figure 1 with 3 supplements
High-throughput profiling of tyrosine kinase substrate specificity using bacterial peptide display.

(A) Schematic representation of the workflow for kinase specificity profiling. (B) Heatmap depicting the specificity of the c-Src kinase domain, measured using the X5-Y-X5 library. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored sequence features, negative value), to white (neutral sequence features, near zero value), to red (favored sequence features, positive value). Values in the heatmap are the average of three replicates. (C) Correlation between position-specific amino acid enrichments from screens with the 4G10 Platinum and PY20 biotinylated pan-phosphotyrosine antibodies.

Figure 1—figure supplement 1
Composition of the X5-Y-X5 library.

(A) Table showing the read counts for all amino acids and the stop codon across all positions in the strep-tagged X5-Y-X5 library, from one sequencing run with an unselected (input) library. (B) Correlation of amino acid frequencies at each position from two replicates of the input library. (C) Distribution of frequencies from two replicates of the input library.

Figure 1—figure supplement 1—source data 1

Counts table corresponding to one sequence run from an input X5-Y-X5 library.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig1-figsupp1-data1-v2.xlsx
Figure 1—figure supplement 2
Phosphorylation of the X5-Y-X5 library by c-Src.

Flow cytometry analysis monitoring the distribution of phosphotyrosine levels over time (left). The mean fluorescence intensities, which represent phosphorylation levels, plotted as a function of time (right).

Figure 1—figure supplement 3
Heatmap and logo depicting the specificity of the c-Src kinase domain, measured using the X5-Y-X5 library.

Only peptides with one central tyrosine were considered in this analysis. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored sequence features, negative value), to white (neutral sequence features, near zero value), to red (favored sequence features, positive value). The same values were used to plot the heatmap and the sequence logo. The height for the central ‘Y’ in the sequence logo is an arbitrary value, chosen for optimal visualization of other features. Values are the average of three replicates.

Figure 2 with 2 supplements
Specificity profiling of tyrosine kinases using the X5-Y-X5 library.

(A) Heatmaps depicting the specificities of c-Abl, Fer, EPHB1, and EPHB2. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored sequence features, negative value), to white (neutral sequence features, near zero value), to red (favored sequence features, positive value). Values in the heatmaps are the average of three replicates. (B) Sequences of consensus peptides identified through X5-Y-X5 screens, compared with previously reported SrcTide and AblTide sequences. (C) Phosphorylation kinetics of five consensus peptides against five kinases. Initial rates were normalized to the rate of the cognate consensus peptide. All peptides were used at a concentration of 100 μM, and the kinases were used at a concentration of 10–50 nM. Error bars represent the standard deviation from at least three measurements.

Figure 2—source data 1

Position-specific amino acid enrichment matrices from the tyrosine kinase X5-Y-X5 library screens.

Matrices calculated with and without inclusion of multi-tyrosine sequences are provided.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Heatmaps and logos depicting the specificities of c-Abl, Fer, EPHB1, and EPHB2.

Only peptides with one central tyrosine were considered in this analysis. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored sequence features, negative value), to white (neutral sequence features, near zero value), to red (favored sequence features, positive value). The same values were used to plot the heatmaps and the sequence logos. The height for the central ‘Y’ in the sequence logos is an arbitrary value, chosen for optimal visualization of other features. Values are the average of three replicates.

Figure 2—figure supplement 2
Phosphorylation kinetics of five consensus peptides against five kinases.

Initial rates measured for each kinase were normalized to the rate of the corresponding consensus peptide. All peptides were used at a concentration of 20 μM, and the kinases were used at a concentration of 10–50 nM. Error bars represent the standard deviation from at least three measurements.

Figure 3 with 1 supplement
Predicting relative phosphorylation rates using data from X5-Y-X5 library screens.

(A) Correlation between measured phosphorylation rates and X5-Y-X5 predictions for 12 peptides with c-Src. All peptides were used at a concentration of 100 μM, and c-Src was used at a concentration of 500 nM. Error bars represent the standard deviation from at least three rate measurements and three separate scores with individual replicates of the X5-Y-X5 screen. (B) Correlation between the magnitude of mutational effects for 6 peptide pairs with mutational effects predicted from X5-Y-X5 library screens. Error bars represent the standard deviation of at least three rate measurements and three separate scores with individual replicates of the X5-Y-X5 screen.

Figure 3—figure supplement 1
Assay to measure peptide phosphorylation rates using reverse-phase HPLC.

Phosphorylation of the CDK5_Y15 peptide (100 μM) by c-Src (500 nM), monitored by RP-HPLC of selected time points. The HPLC chromatogram shows the formation of a phosphorylated species over time, with concomitant loss of the unphosphorylated peptide (left). The area under the two peaks in the chromatogram were quantified and plotted for each time point (right). Initial phosphorylation rates were extracted by fitting a line to the first few timepoints.

Figure 4 with 9 supplements
Specificity profiling of tyrosine kinases using the pTyr-Var library.

(A) Distribution of enrichment scores from pTyr-Var screens with 13 tyrosine kinases. Each point represents a peptide sequence in the pTyr-Var library. Data points in orange-red represent sequences without a Tyr residue and data points in dark gray represent sequences with a Tyr residue. Each dataset represents the average of three to five replicates. (B) Correlation between enrichment scores and measured phosphorylation rates for 12 peptides (100 μM) with c-Src (500 nM). (C) Correlation between the magnitude of mutational effects for 6 peptide pairs in the pTyr-Var library with mutational effects measured using an in vitro kinetic assay. Error bars in panels B and C represent the standard deviation from 3 to 4 rate measurements and four pTyr-Var screens. (D) Matrix of Pearson’s correlation coefficients for all pairwise comparisons between replicate-averaged pTyr-Var datasets for 13 kinases. (E) Volcano plot depicting mutational effects in the pTyr-Var screen with c-Src kinase domain. Data points represent the average of four replicates. Hits are colored orange-red. (F) Percent phosphorylation of SHP2 wild-type, D61V, and D61N (10 μM) after an hour incubation with c-Src, Fyn, and FGFR1 (1 μM). Error bars represent the standard deviation from 2 to 3 measurements.

Figure 4—source data 1

Enrichment scores from tyrosine kinase pTyr-Var screens.

Data are provided in a flat sheet with average and standard deviation values for all kinase-substrate pairs. Data are also provided for each kinase as a side-by-side comparison of enrichment scores reference and variant sequences and whether the mutation was considered a significant in our analysis. Three sheets are provided listing substrates for c-Src, Fyn, and c-Abl that are also found in a curated list of kinase-substrate pairs in the PhosphositePlus database.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig4-data1-v2.xlsx
Figure 4—source data 2

Position-specific amino acid enrichment matrices from the tyrosine kinase pTyr-Var library screens for sequences containing a single central tyrosine residue.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig4-data2-v2.xlsx
Figure 4—figure supplement 1
Properties of the pTyr-Var library.

(A) Frequency of sequences in the library with different numbers of tyrosine residues. (B) Positions of mutations across the library relative to the central tyrosine (zero-position). (C) Frequency of substitutions associated with each phosphosite. (D) Abundance of each possible amino acid substitution across the library.

Figure 4—figure supplement 2
Pre-activation of FGFR1, FGFR3, and MERTK by auto-phosphorylation.

Kinases (25 μM) were incubated with ATP (5 mM) in a magnesium-containing neutral pH buffer for 0.5–2 hr, then desalted and concentrated to remove excess ATP. Proteins were analyzed by electrospray-ionization mass spectrometry. The envelope of multiply-charged states was deconvoluted using the instrument software, and the deconvoluted spectra are shown. The number of phosphorylation events on each kinase is labeled.

Figure 4—figure supplement 3
Matrix of Pearson’s correlation coefficients for all replicates of pTyr-Var screens across all 12 kinases.
Figure 4—figure supplement 4
Assessment of the extent of enrichment in pTyr-Var screens with 12 kinases.

These graphs assess what fraction of the sequences containing no Tyr residue (out of 370 sequences) and what fraction of the sequences containing 1 Tyr residue (out of 7468 sequences) have an enrichment score above the cutoff value indicated on the x-axis.

Figure 4—figure supplement 5
Heatmaps depicting the position-specific amino acid preferences for 12 tyrosine kinase domains, extracted from screens with the pTyr-Var library.

Only sequences with a single central tyrosine were considered in this analysis. Position-specific amino acid enrichment scores were calculated by taking the average log2-transformed enrichment of every sequence with that particular feature. Values are displayed on a color scale from blue (disfavored sequence features, negative value), to white (neutral sequence features, near zero value), to red (favored sequence features, positive value). Values in the heatmaps are the average of three to five replicates.

Figure 4—figure supplement 6
Volcano plots depicting mutational effects in the pTyr-Var screen for 12 kinase domains.

Datasets are the average of three to five replicates. Significant hits are colored in orange-red.

Figure 4—figure supplement 7
Number of significant mutations for each kinase at each position surrounding the central tyrosine residue.

Mutations that added or removed a tyrosine residue were excluded from these counts.

Figure 4—figure supplement 8
Enrichment scores from pTyr-Var screens for phosphorylation of the RET Tyr 981 reference and variant (R982C) peptides by 12 tyrosine kinases.

Error bars represent the standard deviations from three to five replicates.

Figure 4—figure supplement 9
Enrichment scores from pTyr-Var screens for phosphorylation of SHP2 Y62 reference and variant (D61N and D61V) peptides by c-Src, Fyn, and FGFR1.

Error bars represent the standard deviations from three to five replicates.

Figure 5 with 2 supplements
Context-dependent effects of tyrosine kinase recognition.

(A) Correlation of enrichment scores measured for c-Src in the pTyr-Var library screen with scores predicted from the X5-Y-X5 library using a position-specific scoring matrix. (B) Correlation between predicted scores and measured phosphorylation rates for 14 peptides (100 μM) with c-Src (500 nM). Peptides that could not be accurately scored by the X5-Y-X5 data are highlighted in orange. (C) Correlation of variant effects measured in the pTyr-Var library screen with those predicted from the X5-Y-X5 library screen for c-Src. Several points lie in the top-left and bottom-right quadrants, indicating a discrepancy between the measured mutational effect in the pTyr-Var screen and the predicted mutational effect from the X5-Y-X5 screen. (D) Effects of serine-to-proline substitution at the –2 position in various assays with c-Src. The left panels show the enrichment levels of –2 serine and proline in the X5-Y-X5 screen (top), and the effect of a –2 serine to proline substitution in a specific peptide in the pTyr-Var screen, (bottom). The right panels show rate measurements using the RP-HPLC assay for the same substitution in the Src consensus peptide (top) and the peptide from the pTyr-Var screen (bottom).

Figure 5—source data 1

Peptide sequences and their phosphorylation rates by c-Src or c-Abl, measured using the RP-HPLC kinetic assay.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig5-data1-v2.xlsx
Figure 5—source data 2

Mutational effects measured from the pTyr-Var library screens and their corresponding predictions based on the X5-Y-X5 library screening data.

Only those sequence pairs with high-quality sequencing data (read counts >100) and a single central tyrosine were included in the analysis.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig5-data2-v2.xlsx
Figure 5—figure supplement 1
Context-dependent effects of c-Abl substrate recognition.

(A) Correlation of enrichment scores measured for c-Abl in the pTyr-Var library screen with scores predicted from the X5-Y-X5 library using a position-specific scoring matrix. (B) Correlation between predicted scores and measured phosphorylation rates for 4 peptides (100 μM) with c-Abl (500 nM). Peptides that showed significant enrichment in the pTyr-Var screen but lower than expected scores from the X5-Y-X5 data are highlighted in orange.

Figure 5—figure supplement 2
Correlation of variant effects measured in the pTyr-Var library screen with those predicted from the X5-Y-X5 library screen for c-Abl, Fer, EPHB1, and EPHB2.

Several points lie in the top-left and bottom-right quadrant, indicating a discrepancy between the measured mutational effect in the pTyr-Var screen and the predicted mutational effect from the X5-Y-X5 screen.

Figure 6 with 8 supplements
High-throughput profiling of SH2 domain ligand specificity using bacterial peptide display.

(A) Schematic representation of the workflow for SH2 domain specificity profiling. (B) Heatmaps depicting the specificities of the c-Src, SHP2-C, and Grb2 SH2 domains, measured using the X5-Y-X5 library. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored), to white (neutral), to red (favored). Values in the heatmaps are the average of three replicates. (C) Distribution of enrichment scores from pTyr-Var screens with three SH2 domains and the pan-phosphotyrosine antibody 4G10 Platinum. Each point represents a peptide sequence in the library. The antibody selection was done similar to the kinase screens, with antibody labeling of cells, followed by bead-based enrichment, as opposed to cell enrichment with antibody-saturated beads. Each dataset represents the average of three replicates. (D) Correlation between enrichment scores for 9 peptides from the pTyr-Var screen and binding affinities measured using a fluorescence polarization assay. Error bars represent the standard deviations from three screens or binding measurements. (E) Examples of phosphosite-proximal mutations that selectively enhance binding to specific SH2 domains. Error bars represent the standard deviations from three screens.

Figure 6—source data 1

Position-specific amino acid enrichment matrices from the SH2 domain X5-Y-X5 library screens.

Matrices calculated with and without inclusion of multi-tyrosine sequences are provided.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig6-data1-v2.xlsx
Figure 6—source data 2

Enrichment scores from SH2 domain pTyr-Var screens.

Data are provided in a flat sheet with average and standard deviation values for all SH2-ligand pairs. Data are also provided for each SH2 domain as a side-by-side comparison of enrichment scores reference and variant sequences and whether the mutation was considered a significant in our analysis.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig6-data2-v2.xlsx
Figure 6—source data 3

Position-specific amino acid enrichment matrices from the SH2 domain pTyr-Var library screens for sequences containing a single central tyrosine residue.

https://cdn.elifesciences.org/articles/82345/elife-82345-fig6-data3-v2.xlsx
Figure 6—figure supplement 1
Mass spectrometry analysis of biotinylated SH2 domains.

Proteins were analyzed by electrospray-ionization mass spectrometry. The envelope of multiply-charged states was deconvoluted using the instrument software, and the deconvoluted spectra are shown.

Figure 6—figure supplement 2
Flow cytometry analysis of library phosphorylation by a cocktail of tyrosine kinases.

Cells displaying the X5-Y-X5 library were treated with a kinase cocktail containing c-Src, c-Abl, AncSZ, and EPHB1 for 3 hr, then labeled with a pan-phosphotyrosine antibody (PY20 PerCP-eFluor 710) and analyzed by flow cytometry.

Figure 6—figure supplement 3
Heatmaps and logos depicting the specificities of the c-Src, SHP2-C, and Grb2 SH2 domains, measured using the X5-Y-X5 library.

Only peptides with one central tyrosine were considered in this analysis. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored sequence features, negative value), to white (neutral sequence features, near zero value), to red (favored sequence features, positive value). The same values were used to plot the heatmaps and the sequence logos. The height for the central ‘Y’ in the sequence logos is an arbitrary value, chosen for optimal visualization of other features. Values are the average of three replicates.

Figure 6—figure supplement 4
Matrix of Pearson’s correlation coefficients for all replicates of pTyr-Var screens across all 3 SH2 domains and 4G10 platinum.
Figure 6—figure supplement 5
Volcano plots depicting mutational effects in the pTyr-Var screen for 3 SH2 domains.

Datasets are the average of three replicates. Hits are colored in orange-red.

Figure 6—figure supplement 6
Number of significant mutations for each SH2 domain at each position surrounding the central phosphotyrosine residue.

Mutations that added or removed a tyrosine residue are excluded from these counts.

Figure 6—figure supplement 7
Comparison of the pTyr-Var screens for the c-Src kinase and SH2 domains.

Kinase domain data are the average of four replicates, and SH2 data are the average of three replicates.

Figure 6—figure supplement 8
Divergent effects of phosphosite-proximal mutations on c-Src kinase and SH2 domain recognition.

The graph on the left shows the effects of mutations that were significant for the kinase domain (gray) or the SH2 domain (orange-red). The graph on the right shows examples of phosphosite-proximal mutations selectively impact the kinase or SH2 domain of c-Src. Error bars for the kinase and SH2 domain indicate the standard deviations from four and three replicates, respectively.

Figure 7 with 3 supplements
Expansion of peptide display libraries using Amber suppression.

(A) Non-canonical amino acids used in this study. CMF = 4-carboxymethyl phenylalanine, AzF = 4-azido phenylalanine, and AcK = N-ε-acetyl-L-lysine. (B) Amber suppression in the strep-tagged X5-Y-X5 library using CMF. Library surface-display level was monitored by flow cytometry using a fluorophore-labeled StrepMAB antibody for samples with or without Amber suppression components. (C) AzF labeling on bacterial cells using a DIBO-conjugated fluorophore. Cells expressing the X5-Y-X5 library, with and without various Amber suppression components, were treated with DIBO-conjugated Alexa Fluor 555 then analyzed by flow cytometry. (D) Heatmaps depicting the specificities of c-Src, Hck, and c-Abl after CMF or acetyl lysine incorporation. Only sequences with one stop codon were used in this analysis. Enrichment scores were log2-transformed and are displayed on a color scale from blue (disfavored), to white (neutral), to red (favored). Values in heatmaps are the average of three replicates.

Figure 7—figure supplement 1
Stop codon enrichment levels in c-Src X5-Y-X5 screens using different analysis methods.

Error bars represent the standard deviations from three screens.

Figure 7—figure supplement 2
Comparison of position-specific enrichments in screens with Amber suppression analyzed in two different ways.

In each plot, the enrichment of specific amino acids or a stop codon, after phosphorylation by c-Src and bead-based selection, were calculated using two different methods. X-values indicate log-transformed enrichment values calculated across all sequences in the library. Y-values indicate log-transformed enrichment values only for sequences that contain exactly one Amber stop codon. The orange-red points correspond to the Amber codon enrichments at all 10 positions, which selectively fall off of the x=y diagonal line.

Figure 7—figure supplement 3
Phosphorylation kinetics of Lys- and AcK-containing consensus peptides against c-Src and c-Abl.

Initial rates measured for each kinase were normalized to the rate of the corresponding cognate consensus peptide. Peptides were used at a concentration of 100 or 20 μM, and the kinases were used at a concentration of 10–50 nM. Error bars represent the standard deviation from three measurements.

Author response image 1
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Tables

Table 1
Michaelis-Menten parameters for consensus peptides against c-Src and c-Abl kinase domains.

All measurements were carried out using the ADP-Quest assay in three to five replicates. Errors represent the standard error in global fits of all replicates to the Michaelis-Menten equation.

EntryKinasePeptide namePeptide sequencekcat (s–1)KM (μM)
1c-SrcSrc ConsensusGPDECIYDMFPFKKKG4.9±0.4196±38
2c-SrcSrc Consensus (P-5C, D+1 G)GCDECIYGMFPFKKKG4.4±0.297±10
3c-SrcSrcTide (1995)GAEEEIYGEFEAKKKG3.1±0.264±10
4c-SrcSrcTide (2014)GAEEEIYGIFGAKKKG1.8±0.17±3
5c-SrcFer ConsensusGPDEPIYEWWWIKKKG0.4±0.18±4
6c-SrcAbl ConsensusGPDEPIYAVPPIKKKG2.0±0.2159±31
7c-AblAbl ConsensusGPDEPIYAVPPIKKKG3.0±0.26±2
8c-AblAblTide (2014)GAPEVIYATPGAKKKG2.5±0.235±8
Appendix 1—key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (E. coli)MC1061LucigenLucigen: 10361012bacterial cells used for surface-display screens
Strain, strain background (E. coli)DH5αInvitrogenInvitrogen: 18265017bacterial cells used for
general cloning and library cloning
Strain, strain background (E. coli)BL21(DE3)ThermoFisher ScientificThermo: C600003bacterial cells for general protein-expression;
pre-transformed with pCDF-YopH for
tyrosine kinase overexpression
Strain, strain background (E. coli)C43(DE3)LucigenLucigen: NC9581214bacterial cells used for SH2 domain over-expression;
pre-transformed with pCDFDuet-BirA-WT for biotinylation
Antibody4 G10 Platinum, Biotin (mouse monoclonal)Millipore SigmaMillipore Sigma: 16–452-MIbiotin conjugated mouse monoclonal
pan-phosphotyrosine antibody dilution: (1:1000)
AntibodyPY20-PerCP-eFluor 710 (mouse monoclonal)eBioscienceeBioscience: 46-5001-42PerCP-eFluor 710-conjugated mouse monoclonal
pan-phosphotyrosine antibody, clone PY20 dilution: (1:25)
AntibodyPY20-biotin (mouse monoclonal)ExalphaExalpha: 50-210-1865biotin conjugated mouse monoclonal
pan-phosphotyrosine antibody dilution (1:500)
AntibodyStrepMAB Chromeo 488 (mouse monoclonal)IBA LifeSciencesIBA: 2-1546-050Chromeo 488-conjugated antibody that
recognizes the strep-tag dilution: (1:50–100).
Discontinued, but can be replaced with IBA
LifeSciences StrepMAB-Classic conjugate
DY-488 (IBA: 2-1563-050)
Recombinant DNA reagentpBAD33-eCPXPMID:18480093Addgene: 23336pBAD33 plasmid encoding the eCPX bacterial
display gene with flanking 5' and 3' SfiI restriction sites
Recombinant DNA reagentpBAD33-eCPX-cStrepPMID:29547119
pBAD33 plasmid encoding the eCPX bacterial
display gene with a 3' sequence encoding a
strep-tag and flanking 5' and 3' SfiI restriction sites
Recombinant DNA reagentpBAD33-eCPX-cMycthis paper
pBAD33 plasmid encoding the eCPX bacterial
display gene with a 3' sequence encoding a
myc-tag and flanking 5' and 3' SfiI restriction sites
Recombinant DNA reagentX5-Y-X5 Library (myc-tagged)this paper
peptide display library in the pBAD33 vector, fused
to the eCPX scaffold, containing 1–10 million
unique sequences with the structure X5-Y-X5, where X is
encoded by an NNS codon. The scaffold protein is
encoded to have a C-terminal myc-tag: EQKLISEEDL.
Recombinant DNA reagentX5-Y-X5 Library (strep-tagged)this paper
peptide display library in the pBAD33 vector, fused to
the eCPX scaffold, containing 1–10 million unique
sequences with the structure X5-Y-X5,
where X is encoded by an NNS codon.
The scaffold protein is encoded to have a
C-terminal strep-tag: WSHPQFEK.
Recombinant DNA reagentpTyr-Var Library (myc-tagged)this paper
peptide display library in the pBAD33 vector,
fused to the eCPX scaffold, containing ~10,000
unique sequences encoding reference and
variant phosphosite pairs deried from the
PhosphoSitePlus database. The scaffold
protein is encoded to have a C-terminal
myc-tag: EQKLISEEDL.
Recombinant DNA reagentpTyr-Var Library (strep-tagged)this paper
peptide display library in the pBAD33 vector,
fused to the eCPX scaffold, containing ~10,000
unique sequences encoding reference and variant
phosphosite pairs deried from the
PhosphoSitePlus database. The scaffold protein is
encoded to have a C-terminal strep-tag: WSHPQFEK.
Recombinant DNA reagentpET-23a-His6-TEV-Src(KD)PMID:29547119
bacterial expression vector encoding the human
c-Src kinase domain (residues 260–528), with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-23a-His6-TEV-Fyn(KD)PMID:29547119
bacterial expression vector encoding the human
Fyn kinase domain (residues 261–529) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-23a-His6-TEV-Hck(KD)PMID:29547119
bacterial expression vector encoding the human
Hck kinase domain (residues 252–520) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-23a-His6-TEV-Abl(KD)PMID:29547119
bacterial expression vector encoding the mouse
c-Abl kinase domain (residues 232–502) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-23a-His6-TEV-AncSZ(KD)DOI:
10.1101/2022.04.24.489292

bacterial expression vector encoding the AncSZ
kinase domain (residues 352–627) with an N-terminal
His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET23a-His6-TEV-Fer(KD)this paper
bacterial expression vector encoding the mouse
Fer kinase domain (residues 553–823) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-His6-TEV-FGFR1(KD)PMID:30004690Addgene: 79719bacterial expression vector encoding the human
FGFR1 kinase domain (residues 456–763) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-His6-TEV-FGFR3(KD)PMID:30004690Addgene: 79731bacterial expression vector encoding the human
FGFR3 kinase domain (residues 449–759) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-His6-TEV-EPHB1(KD)PMID:30004690Addgene: 79694bacterial expression vector encoding the human
EPHB1 kinase domain (residues 602–896) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-His6-TEV-EPHB2(KD)PMID:30004690Addgene: 79697bacterial expression vector encoding the human
EPHB2 kinase domain (residues 604–898) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpET-His6-TEV-MERTK(KD)PMID:30004690Addgene: 79705bacterial expression vector encoding the human
MERTK kinase domain (residues 570–864) with an
N-terminal His6-tag and TEV protease recognition sequence
Recombinant DNA reagentpCDF-YopHPMID:16260764
bacterial expression vector for co-expression of
untagged YopH phosphatase with tyrosine kinases
Recombinant DNA reagentpET28-His6-TEV-SHP2-C459E-no tailthis paper
bacterial expression vector encoding the human SHP2
(residues 1–526) with the C459E mutation, an N-terminal
His6-tag, and TEV protease recognition sequence
Recombinant DNA reagentpET28-His6-TEV-SHP2-C459E-no tail-D61Vthis paper
bacterial expression vector encoding the human SHP2
(residues 1–526) with C459E and D61V mutations, an
N-terminal His6-tag, and TEV protease recognition sequence
Recombinant DNA reagentpET28-His6-TEV-SHP2-C459E-no tail-D61Nthis paper
bacterial expression vector encoding the human
SHP2 (residues 1–526) with C459E and D61N mutations,
an N-terminal His6-tag, and TEV protease recognition sequence
Recombinant DNA reagentpCDFDuet-BirA-WTthis paper
bacterial expression vector encoding BirA biotin ligase,
used to coexpress with SH2 domain expression
vector for biotinylation of SH2 domain
Recombinant DNA reagentpET-His6-SUMO-Src(SH2)this paper
bacterial expression vector encoding the human
cSrc SH2 domain (residues 143–250) with an
N-terminal His6-SUMO tag
Recombinant DNA reagentpET-His6-SUMO-SHP2(CSH2)this paper
bacterial expression vector encoding the human SHP2
CSH2 domain (residues 105–220) with an N-terminal His6-SUMO tag
Recombinant DNA reagentpET-His6-SUMO-Grb2(SH2)this paper
bacterial expression vector encoding the human Grb2
SH2 domain (residues 56–152) with an N-terminal His6-SUMO tag
Recombinant DNA reagentpULTRA CMFPMID:28604693
bacterial expression vector encoding the tRNA/syntetase
pair for incorporation of 4-carboxymethyl phenylalanine
via Amber suppression
Recombinant DNA reagentpEVOL pAzFRS.2.t1PMID:26571098Addgene: 73546bacterial expression vector encoding the tRNA/syntetase
pair for incorporation of 4-azido phenylalanine and other
Phe derivatives via Amber suppression
Recombinant DNA reagentpULTRA chAcKRS3PMID:29544052
bacterial expression vector encoding the tRNA/syntetase
pair for incorporation of acetyl-lysine via Amber suppression;
gift from Abhishek Chatterjee at Boston College
Recombinant DNA reagentpULTRA-Amp CMFthis paper
bacterial expression vector encoding the tRNA/syntetase
pair for incorporation of 4-carboxymethyl phenylalanine
via Amber suppression, altered to have an ampicillin resistance marker
Recombinant DNA reagentpULTRA-Amp pAzFRS.2.t1this paper
bacterial expression vector encoding the tRNA/syntetase
pair for incorporation of 4-azido phenylalanine and other
Phe derivatives via Amber suppression, altered to have
an ampicillin resistance marker
Recombinant DNA reagentpULTRA-Amp chAcKRS3this paper
bacterial expression vector encoding the tRNA/syntetase
pair for incorporation of acetyl-lysine via Amber suppression,
altered to have an ampicillin resistance marker
Sequence-based reagentX5-Y-X5 library oligo; eCPX-rand-libthis paper, purchased from Millipore Sigma
primer sequence: 5’-GCTGGCCAGTCTGGCCAGNNS
NNSNNSNNSNNStatNNSNNSNNSNNSNNSGGAGG
GCAGTCTGGGCAGTCTG 3’
Sequence-based reagentOligopool-fwd-primerthis paper, purchased from Millipore Sigma
primer sequence: 5’-GCTGGCCAGTCTG-3’
Sequence-based reagentOligopool-rev-primerthis paper, purchased from Millipore Sigma
primer sequence: 5’-CAGACTGCCCAGACT-3’
Sequence-based reagentlink-eCPX-fwdthis paper, purchased from Millipore Sigma
5’-GGAGGGCAGTCTGGGCAGTCTG-3’
Sequence-based reagentlink-eCPX-revthis paper, purchased from Millipore Sigma
5’-GCTTGGCCACCTTGGCCTTATTA-3’
Sequence-based reagentBB-fwd-primerthis paper, purchased from Millipore Sigma
5’-TAATAAGGCCAAGGTGGCCAAGC-3’
Sequence-based reagentBB-rev primerthis paper, purchased from Millipore Sigma
5’-CTGGCCAGACTGGCCAGCTACG-3’
Sequence-based reagentTruSeq-eCPX-Fwdsequence from PMID:29547119, purchased from Millipore Sigmaround one amplicon PCR primerprimer sequence: 5’-TGACTGGAGTTCAGACGTG
TGCTCTTCCGATCTNNNNNNACCGCA
GGTACTTCCGTAGCT-3’
Sequence-based reagentTruSeq-eCPX-Revsequence from PMID:29547119, purchased from Millipore Sigmaround one amplicon PCR primerprimer sequence: 5’-CACTCTTTCCCTACACGACG
CTCTTCCGATCTNNNNNN
TTTTGTTGTAGTCACCAGACTG-3’
Sequence-based reagentD701sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGACGG
CATACGAGATcgagtaatGTG
ACTGGAGTTCAGACGTG-3'
Sequence-based reagentD702sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGA
CGGCATACGAGATtctccgga
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD703sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGA
CGGCATACGAGATaatgagcg
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD704sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGAC
GGCATACGAGATggaatctcG
TGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD705sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGA
AGACGGCATACGAGA
TttctgaatGTGACTGGAGT
TCAGACGTG-3'
Sequence-based reagentD706sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGA
CGGCATACGAGATacgaattc
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD707sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAG
ACGGCATACGAGATagcttcag
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD708sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGACG
GCATACGAGATgcgcattaGT
GACTGGAGTTCAGACGTG-3'
Sequence-based reagentD709sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAG
ACGGCATACGAGATcatagccg
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD710sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGA
AGACGGCATACGAGATttcgcgga
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD711sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAAGACG
GCATACGAGATgcgcgaga
GTGACTGGAGTTCAGACGTG-3'
Sequence-based reagentD712sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-CAAGCAGAA
GACGGCATACGAGATctatcgctGT
GACTGGAGTTCAGACGTG-3'
Sequence-based reagentD501sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGGCGA
CCACCGAGATCTACACtatagcct
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD502sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGGCG
ACCACCGAGATCTACACatagaggc
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD503sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGGCGA
CCACCGAGATCTACACcctatcct
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD504sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGGCGA
CCACCGAGATCTACACggctctga
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD505sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGGC
GACCACCGAGATCTACACaggcgaag
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD506sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGG
CGACCACCGAGATCTACACtaatctta
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD507sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACGGC
GACCACCGAGATCTACACcaggacgt
ACACTCTTTCCCTACACGAC-3'
Sequence-based reagentD508sequence from Illumina, purchased from Millipore Sigmaround two amplicon/indexing PCR primerprimer sequence: 5'-AATGATACG
GCGACCACCGAGATCTACAC
gtactgacACACTCTTTCCCTACACGAC-3'
Peptide, recombinant proteinSrc(KD)this paper, expressed/purified in-house
human c-Src kinase domain (residues 260–528)
Peptide, recombinant proteinFyn(KD)this paper, expressed/purified in-house
human Fyn kinase domain (residues 261–529)
Peptide, recombinant proteinHck(KD)this paper, expressed/purified in-house
human Hck kinase domain (residues 252–520)
Peptide, recombinant proteinAbl(KD)this paper, expressed/purified in-house
mouse c-Abl kinase domain (residues 232–502)
Peptide, recombinant proteinJAK2 Protein, activeMillipore SigmaMillipore Sigma: 14–640 MActive, C-terminal His6-tagged,
recombinant, human JAK2, amino
acids 808-end, expressed by baculo
virus in Sf21 cells, for use in Enzyme Assays.
Peptide, recombinant proteinAncSZ(KD)this paper, expressed/purified in-house
AncSZ kinase domain (residues 352–627)
designed by ancestral sequence reconstruction
Peptide, recombinant proteinFer(KD)this paper, expressed/purified in-house
mouse Fer kinase domain (residues 553–823)
Peptide, recombinant proteinFGFR1(KD)this paper, expressed/purified in-house
human FGFR1 kinase domain (residues 456–763)
Peptide, recombinant proteinFGFR3(KD)this paper, expressed/purified in-house
human FGFR3 kinase domain (residues 449–759)
Peptide, recombinant proteinEPHB1(KD)this paper, expressed/purified in-house
human EPHB1 kinase domain (residues 602–896)
Peptide, recombinant proteinEPHB2(KD)this paper, expressed/purified in-house
human EPHB2 kinase domain (residues 604–898)
Peptide, recombinant proteinMERTK(KD)this paper, expressed/purified in-house
human MERTK kinase domain (residues 570–864)
Peptide, recombinant proteinSrc(SH2)this paper, expressed/purified in-house
human c-Src SH2 domain (residues 143–250)
Peptide, recombinant proteinSHP2(C-SH2)this paper, expressed/purified in-house
human SHP2 C-SH2 domain (residues 105–220)
Peptide, recombinant proteinGrb2(SH2)this paper, expressed/purified in-house
human Grb2 SH2 domain (residues 56–152)
Peptide, recombinant proteinSHP2(PTP; C459E)this paper, expressed/purified in-house
human full-length SHP2 (residues 1–526; C459E)
Peptide, recombinant proteinSHP2(PTP; C459E, D61V)this paper, expressed/purified in-house
human full-length SHP2 (residues 1–526; C459E, D61V)
Peptide, recombinant proteinSHP2(PTP; C459E, D61N)this paper, expressed/purified in-house
human full-length SHP2 (residues 1–526; C459E, D61N)
Peptide, recombinant proteinSHP2(PTP; C459E, G60V)this paper, expressed/purified in-house
human full-length SHP2 (residues 1–526; C459E, G60V)
Peptide, recombinant proteinSrc Consensusthis paper, synthesized in-house
peptide sequence: Ac-GPDECIYDMFPFKKKG-NH2
Peptide, recombinant proteinSrc Consensus (P-5C, D+1 G)this paper, synthesized in-house
peptide sequence: Ac-GCDECIYGMFPFRRRG-NH2
Peptide, recombinant proteinAbl Consensusthis paper, synthesized in-house
peptide sequence: Ac-GPDEPIYAVPPIKKKG-NH2
Peptide, recombinant proteinFer Consensusthis paper, synthesized in-house
peptide sequence: Ac-GPDEPIYEWWWIKKKG-NH2
Peptide, recombinant proteinEPHB1 Consensusthis paper, synthesized in-house
peptide sequence: Ac-GPPEPNYEVIPPKKKG-NH2
Peptide, recombinant proteinEPHB2 Consensusthis paper, synthesized in-house
peptide sequence: Ac-GPPEPIYEVPPPKKKG-NH2
Peptide, recombinant proteinSrcTide (1995)sequence from PMID:7845468, synthesized in-house
peptide sequence: Ac-GAEEEIYGEFEAKKKG-NH2
Peptide, recombinant proteinSrcTide (2014)sequence from PMID:25164267, purchased from Synpeptide
peptide sequence: Ac-GAEEEIYGIFGAKKKG-NH2
Peptide, recombinant proteinAblTide (2014)sequence from PMID:7845468, synthesized in-house
peptide sequence: Ac-GAPEVIYATPGAKKKG-NH2
Peptide, recombinant proteinHRAS_Y64sequence from PMID:35606422, purchased from Synpeptide
peptide sequence: Ac-AGQEEYSAMRD-NH2
Peptide, recombinant proteinHRAS_Y64_E63Ksequence from PMID:35606422, purchased from Synpeptide
peptide sequence: Ac-AGQEKYSAMRD-NH2
Peptide, recombinant proteinCDK13_Y716_YFthis paper, synthesized in-house
peptide sequence: Ac-IGEGTYGQVFK-NH2
Peptide, recombinant proteinCDK13_Y716_G717R_YFthis paper, synthesized in-house
peptide sequence: Ac-IGEGTYRQVFK-NH2
Peptide, recombinant proteinCDK5_Y15sequence from PMID:35606422, purchased from Synpeptide
peptide sequence: Ac-IGEGTYGTVFK-NH2
Peptide, recombinant proteinCDK5_Y15_G16Rsequence from PMID:35606422, purchased from Synpeptide
peptide sequence: Ac-IGEGTYRTVFK-NH2
Peptide, recombinant proteinPLCG1_Y210this paper, synthesized in-house
peptide sequence: Ac-SGDITYGQFAQ-NH2
Peptide, recombinant proteinPLCG1_Y210_T209Nthis paper, synthesized in-house
peptide sequence: Ac-SGDINYGQFAQ-NH2
Peptide, recombinant proteinGLB1_Y294this paper, synthesized in-house
peptide sequence: Ac-VASSLYDILAR-NH2
Peptide, recombinant proteinGLB1_Y294_L297Fthis paper, synthesized in-house
peptide sequence: Ac-VASSLYDIFAR-NH2
Peptide, recombinant proteinMISP_Y95this paper, synthesized in-house
peptide sequence: Ac-EGWQVYRLGAR-NH2
Peptide, recombinant proteinHLA-DPB1_Y59_F64L_YFthis paper, synthesized in-house
peptide sequence: Ac-LERFIYNREEL-NH2
Peptide, recombinant proteinPEAK1_Y797this paper, synthesized in-house
peptide sequence: Ac-SVEELYAIPPD-NH2
Peptide, recombinant proteinSIRPA_Y496_P491Lthis paper, synthesized in-house
peptide sequence: Ac-LFSEYASVQV-NH2
Peptide, recombinant proteinHGD_Y166_F169Lthis paper, synthesized in-house
peptide sequence: Ac-GNLLIYTELGK-NH2
Peptide, recombinant proteinITGA3_Y237_YFthis paper, synthesized in-house
peptide sequence: Ac-WDLSEYSFKDP-NH2
Peptide, recombinant proteinITGA3_Y237_S235P_YFthis paper, synthesized in-house
peptide sequence: Ac-WDLPEYSFKDP-NH2
Peptide, recombinant proteinSrc Consensus (C-2S)this paper, synthesized in-house
peptide sequence: Ac-GPDESIYDMFPFKKKG-NH2
Peptide, recombinant proteinSrc Consensus (C-2P)this paper, synthesized in-house
peptide sequence: Ac-GPDEPIYDMFPFKKKG-NH2
Peptide, recombinant proteinACTA1_Y171_YFthis paper, synthesized in-house
peptide sequence: Ac-QPIFEG(pY)ALPHAG-NH2
Peptide, recombinant proteinACTA1_Y171_A172G_YFthis paper, synthesized in-house
peptide sequence: Ac-QPIFEG(pY)GLPHAG-NH2
Peptide, recombinant proteinACTB_Y240this paper, synthesized in-house
peptide sequence: Ac-QSLEKS(pY)ELPDGG-NH2
Peptide, recombinant proteinACTB_Y240_P243Lthis paper, synthesized in-house
peptide sequence: Ac-QSLEKS(pY)ELLDGG-NH2
Peptide, recombinant proteinCCDC39_Y593this paper, synthesized in-house
peptide sequence: Ac-QRKQQL(pY)TAMEEG-NH2
Peptide, recombinant proteinCLIP2_Y972this paper, synthesized in-house
peptide sequence: Ac-QSDQRR(pY)SLIDRG-NH2
Peptide, recombinant proteinCLIP2_Y972_R977Pthis paper, synthesized in-house
peptide sequence: Ac-QSDQRR(pY)SLIDPG-NH2
Peptide, recombinant proteinCBS_Y308this paper, synthesized in-house
peptide sequence: Ac-QVEGIG(pY)DFIPTG-NH2
Peptide, recombinant proteinCBS_Y308_G307Sthis paper, synthesized in-house
peptide sequence: Ac-QVEGIS(pY)DFIPTG-NH2
Peptide, recombinant proteinfluorescently-labeled c-Src-SH2 consensus peptidesequence from PMID:7680959
peptide sequence: FITC-Ahx-GDG(pY)EEISPLLL-NH2; gift from Jeanine Amacher at Western Washignton University
Peptide, recombinant proteinSrc Consensus (D+1 K)this paper, synthesized in-house
peptide sequence: Ac-GPDECIYKMFPFKKKG-NH2
Peptide, recombinant proteinSrc Consensus (D1AcK)this paper, synthesized in-house
peptide sequence: Ac-GPDECIY(AcK)MFPFKKKG-NH2
Peptide, recombinant proteinSrc Consensus (C-2K)this paper, synthesized in-house
peptide sequence: Ac-GPDEKIYDMFPFKKKG-NH2
Peptide, recombinant proteinSrc Consensus (C-2AcK)this paper, synthesized in-house
peptide sequence: Ac-GPDE(AcK)IYDMFPFKKKG-NH2
Peptide, recombinant proteinAbl Consensus (A+1 K)this paper, synthesized in-house
peptide sequence: Ac-GPDEPIYKVPPIKKKG-NH2
Peptide, recombinant proteinAbl Consensus (A+1 AcK)this paper, synthesized in-house
peptide sequence: Ac-GPDEPIY(AcK)VPPIKKKG-NH2
Peptide, recombinant proteinAbl Consensus (I+5 K)this paper, synthesized in-house
peptide sequence: Ac-GPDEPIYAVPPKKKKG-NH2
Peptide, recombinant proteinAbl Consensus (I+5 AcK)this paper, synthesized in-house
peptide sequence: Ac-GPDEPIYAVPP(AcK)KKKG-NH2
Commercial assay or kitMiSeq Reagent Kit v3 (150 cycles)IlluminaIllumina:
MS-102–3001

Commercial assay or kitNextSeq 500 Mid-Output v2 Kit (150 cycles)IlluminaIllumina:
FC-404–2001

Commercial assay or kitPromega QuantiFluor dsDNA Sample KitPromegaPromega:
E2671

Commercial assay or kitADP Quest Assay KitEurofins DiscoverxEurofins Discoverx:
90–0071

Commercial assay or kitDynabeads FlowComp Flexi KitThermoFisher ScientificThermoFisher Scientific:
11061D

Chemical compound, drug4-carboxymethyl phenylalanine (CMF)Millipore SigmaMillipore
Sigma:
ENA423210770

Chemical compound, drug4-azido-L-phenylalanine (AzF)Chem-Impex InternationalChem-Impex:
06162

Chemical compound, drugN-ε-Acetyl-L-Lysine (AcK)MP BiomedicalsMP
Biomedicals:
02150235.2

Chemical compound, drugClick-iT sDIBO -Alexa fluor 555ThermoFisherThermo: C20021
OtherCreatine Phosphokinase from rabbit muscleMillipore SigmaMillipore Sigma:
C3755-500UN
purified enzyme extracted from rabbit muscle
Software, algorithmFLASH (version FLASH2-2.2.00)PMID:21903629
https://ccb.jhu.edu/software/FLASH/
Software, algorithmCutadapt (version 3.5)DOI:10.14806/ej.17.1.200
https://cutadapt.readthedocs.io/en/stable/
Software, algorithmPython scripts for processing and analysis of adeep sequencing datathis paper (Li et al., 2023)
https://github.com/nshahlab/2022_Li-et-al_peptide-display
Software, algorithmLogomakerPMID:31821414
https://logomaker.readthedocs.io/en/latest/index.html

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  1. Allyson Li
  2. Rashmi Voleti
  3. Minhee Lee
  4. Dejan Gagoski
  5. Neel H Shah
(2023)
High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display
eLife 12:e82345.
https://doi.org/10.7554/eLife.82345