Supporting Information MALDI versus ESI the impact of the ion source on peptide identification

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1 Supporting Information MALDI versus ESI the impact of the ion source on peptide identification Wiebke Maria Nadler, 1 Dietmar Waidelich, 2 Alexander Kerner, 1 Sabrina Hanke, 1 Regina Berg, 3 Andreas Trumpp 1 and Christoph Rösli*,1,4 1 German Cancer Research Center and HI-STEM ggmbh, Im Neuenheimer Feld 280, Heidelberg, Germany 2 SCIEX Germany GmbH, Landwehrstraße 54, Darmstadt, Germany 3 Department of Chemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland 4 Current address: Novartis Pharma AG, Werk Klybeck, 4057 Basel, Switzerland *christophroesli@gmail.com, telephone , fax Content SI 1 Sample Preparation 2 MALDI Spotting Scheme 3 Monitoring of the Pooling Algorithm 3.1 Differential Identification of Proteins/Peptides per Pooled Fraction 3.2 Protein Masses per Pooled Fraction 4 Impact of the Ion Source on Protein and Peptide Identification 4.1 Protein IDs, Peptide IDs and Spectral Identification Rates 4.2 Representation of Proteins with Different Masses 4.3 Representation of Proteins with Different Abundances 4.4 Identification of Peptides without H, K, and R 5 Characterization of Biological Replicates S-1

2 1 Sample Preparation Unless indicated otherwise, percentages are given as v/v. The volume for destaining, washing, reduction, alkylation and dehydration solutions was 1 ml per Eppendorf tube. 2 MALDI Spotting Scheme Peptide spike-in standards were purchased from PSL and dissolved in CHCA matrix (Promega, 3 mg/ml in 80 % ACN) for automated deposition on MALDI target plates. The fractionation process was started with a manually adjusted post-injection delay of approx. 10 min and matrix was delivered with a flow rate of 2 µl/min. The time for collection of a single fraction was set to 4 seconds, yielding a fraction volume of 180 nl (46.66 nl sample in mobile phase nl matrix). After 80 minutes, the spotting was stopped. For the given spotting schemes one spot contained the respective amount of standard peptide as shown in table S-1. Table S-1 Internal standard spike-in peptides Peptide Sequence m/z nmol/ml matrix fmol/spot Pep-4 TGVFDEAIRTVGF PDE9A-pep1 CLEHMYHDLGLVRDF VN-2 EEQPSTPAPKVEQQEEILC Pep 5 TVFDEAIR Monitoring of the Pooling Algorithm 3.1 Differential Identification of Proteins/Peptides per Pooled Fraction Figure S-1 b shows a significant disparity in differential protein IDs in early fractions compared to late fractions when ESI and MALDI-based analyses identify nearly the same number of proteins. While the main variable between early and late fractions is protein size, instruments with lower absolute ID rates (here the MALDI instrument) might profit more from the increased protein size in the late fractions. Increasing protein size correlates with a higher number of hypothetical peptides per protein, thereby raising the chance to detect at least one of these peptides. S-2

3 a b Peptide IDs [# ESI - # MALDI] Protein IDs [# ESI - # MALDI] c d Figure S-1 Differential identification of proteins (a, b) and peptides (c, d) per pooled gel fraction from MALDI and ESI-based analyses. (a, c) mean with SD, n = 4. (b, d) median with IQR, n = 6. The average difference in protein (b) or peptide (d) identifications between the techniques was calculated for each pooled fraction. Each fraction (except #7) was then classified either as early (#1 #6) or late (#8 #13) fraction. Statistical significance of the disparity between the differential IDs of early and late fractions was determined using an unpaired t-test (two-tailed, **p < ). 3.2 Protein Masses per Pooled Fraction Figure S-2 Scatter dot plots showing the protein masses detected per gel fraction for HPNE, PACO2 and PACO7. A BioStep lane picker was applied for slicing of the gel with HPNE lysate, while a similar tool build in-house was used for the PACO samples. S-3

4 4 Impact of the Ion Source on Protein and Peptide Identification 4.1 Protein IDs, Peptide IDs and Spectral Identification Rates a b c Protein IDs Peptide IDs Identified Spectra in % Figure S-3 Count of proteins (a) peptides (b) and spectra (c) identified per cell line with different instrumental setups (mean with SEM, n = 4). 4.2 Representation of Proteins with Different Masses With respect to protein size distribution there is no obvious difference between the two ion source setups. (Figure S- 4). For both techniques, there is an inherent bias against small proteins as they yield a lower number of distinct peptides. In addition, proteins below a certain threshold are not efficiently trapped in the gel. Figure S-4 Frequency of the log-transformed protein masses for the human SwissProt database and combined protein data from all cell lines detected with ESI or MALDI. 4.3 Representation of Proteins with Different Abundances Figure S-5 shows the relative frequency distribution of proteins with differential abundance of the corresponding gene. Independent of the ionization technique, protein products from genes with high abundance are overrepresented, whereas a low gene expression results in a decreased chance for mass spectrometric identification of the corresponding protein. S-4

5 20 15 MicroArray ESI MALDI Bin Center of Gene Abundance Figure S-5 Relative frequency of identified proteins with different abundances of the corresponding gene (mean with SD, n = 3). Microarray gene expression data for PACO2, PACO3 and PACO7 were provided by Noll et al. (Nat. Med. 2016) and processed with R version Probes mapping to multiple genes were excluded and probe sets were collapsed by retaining only the first probe per gene. Abundance values for each target gene of the microarray were obtained as glog2-transformed average probe intensity across all three cell lines. For the protein dataset, gene names were used as identifiers and duplicates (e.g. from isoforms) were manually removed by retaining the form with the highest number of absolute identifications across samples. Obtained gene abundance values were then annotated to each protein identified per PACO cell line and ion source to calculate the relative frequency distribution of abundance values for each sample. In total, gene expression data could be retrieved for 6265 proteins. 4.4 Identification of Peptides without H, K, and R Figure S-6 Relative percentage of peptides without histidine, arginine and lysine, identified with ESI and MALDI (mean with SD, n = 4). S-5

6 5 Characterization of Biological Replicates a b Subset Proteins % PACO7 PACO3 HPNE & PACO2 & PACO3 & PACO HPNE & PACO2 & PACO HPNE & PACO2 & PACO HPNE 5% 5.8% PACO2 HPNE & PACO3 & PACO PACO2 & PACO3 & PACO % 3.2% 4.3% HPNE & PACO HPNE & PACO % 1.3% 13.9% 6.6% HPNE & PACO PACO2 & PACO PACO2 & PACO PACO3 & PACO HPNE ONLY PACO2 ONLY % % 2.6% % PACO3 ONLY PACO7 ONLY Sum Figure S-7 Table (a) and VENN diagramm (b) showing the overlap between biological replicates in % for proteins with 1 proteotypic peptide for pooled data from MALDI and ESI-based analysis. S-6