Data from: Enabling proteomic studies with RNA-Seq: the proteome of tomato pollen as a test case

The data set included here is the supporting material to the article, "Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case." 2012.

Researchers conducted a quantitative analysis of the proteomes of pollen from domesticated tomato (Solanum lycopersicum) and two wild relatives that exhibit differences in mating systems and in inter-specific reproductive barriers.

Using a custom tomato RNA-Seq database created through 454 pyrosequencing, more than 1200 proteins were identified, with subsets showing expression differences between genotypes or in the accumulation of the corresponding transcripts.

Importantly, no major qualitative or quantitative differences were observed in the characterized proteomes when mass spectra were used to interrogate either a highly curated community database of tomato DNA sequences generated through traditional sequencing technologies, or the RNA-Seq database.

They conclude that RNA-Seq provides a cost-effective and robust platform for protein identification and will be increasingly valuable to the field of proteomics.

This dataset consists of 10 tables containing protein, peptides, and spectral data.

• Resource Title: Lists and classification of tomato pollen proteins from 454 experiments: Tables S1 to S10 (.xls file).

  File Name: pmic7005-sup-0001-tables1.xls

  Resource Description:

  This spreadsheet, 'pmic7005-sup-0001-tables1.xls" contains the ten tables described at the publisher's site. At the publisher's site, it is linked ten times, once for each table. It is listed once here in this record. List of tables:

  Table S1. Statistical analyses related to average length of RNA sequences obtained from 454 sequencing experiments performed to create the different 454 databases

  Table S2: Raw Data from peptides identified in the 3 replicates (R1, R2, R3) using the 3 databases SGN, 454db1, and 454db2. S2 a: SGNdb_R1; S2b: SGNdb_R2; S2 c: SGNdb_R3; S2 d: 454db1_R1; S2e: 454db1_R2; S2f: 454db1_R3; S2 g: 454db2_R1; S2 h: 454db2_R2; S21: 454db2_R3. (file “LopezCasado_Proteomics_SuppTable_S2” at ftp://ted.bti.cornell.edu/pub/tomato_454_unigene)

  Table S3. Numbers of proteins, peptide, and identified spectra in tomato pollen proteome using SGN db and 454 generated databases (454 db1 and 454 db2), considering biological modifications (bm) as an option when performing the search against specific database. R1, R2, and R3 indicate three independent biological replicates

  Table S4. Table S5. Number of proteins, distinct peptides, and spectral identified at three false discovery rate (FDR) level

  Table S5. Functional classification of tomato pollen proteins using iTRAQ and SGN db interrogation

  Table S6. Functional classification of tomato pollen proteins using iTRAQ and 454 db2 interrogation

  Table S7. Proteins differentially expressed in one specific genotype and found in one or more biological replicates using SGN db

  Table S8. Proteins differentially expressed in one specific genotype and found in one or more biological replicates using 454 db2

  Table S9. Proteins differentially expressed in any specific genotype, identified using both SGN db and 454 db2. Each protein showed a >2-fold expression (p-value <0.05) in one genotype compared with the other three, and detected at least in two of the three iTRAQ experimental replicates. SD, standard deviation

  Table S10. Proteins differentially expressed in pair-wise comparisons of genotypes, identified using both SGN db and 454 db2. Each protein showed a >2-fold expression (p < 0.05) in one genotype compared with one other genotype, and was detected in at least two of the three iTRAQ experiment replicates. Ratio refers to relative abundance between the genotypes indicated. SD, standard deviation

  Note: tables S2, S3, & S10 are missing from this and the source version of the spreadsheet, the contact has acknowledged this . 04/2015




• Resource Title: Data Dictionary - Lists and classification of tomato pollen proteins from 454 experiments.

  File Name: Data Dictionary - data enabling proteomic studies rna seq.csv