Each file contains peptides from zone, tip and root samples. The text files contain peptides, peptide counts and the corresponding transcript (see downloads). The first column gives the tissue and run numbers, e.g. "atN" is rhizome tip, run N. The other tissue labels are "ez" for zone, and "r" for root.

Links will be added to the PAVE queryable database of transcripts and peptides as they become available.

Species	Peptide File	PAVE database
Reed Phragmites australis PaR	PaR	Assemblies
Horsetail "scouring rush" Equisetum hymale EhR	EhR
Red rice Oryza longistaminata OlR	OlR
Ginger Zingiber officinale (Line: GW) ZoR	ZoR
Cogongrass Imperata cylindrica IcR	IcR
Spatterdock Nuphar polysepala IcR	NaR
Quackgrass Elytrigia repens ErR	ErR

Methods

• Description: Identification and quantification of proteins in the apical tip and elongation zone of rhizomes; and roots
• Protein extraction: Phenol-based protein extraction
• Pre-fractionation and protein digestion: 12%SDS-PAGE, in gel trypsin digestion
• Mass spectrometry data acquisition: LC-ESI-CID-MS/MS (LTQ), DDA experiment, fragmentation of top 7 peptide ions per cycle
• Peak list generator: extract_msn.exe
• Search algorithm: Sequest
• Database: translated PaRi (PaRi_unitrans_longest_rand.fasta):contigs+singles; 1assembly=1entry; 233,944 target+decoy entries
• Data filtering: SePro 1.0.0.47
• Parameters:
  • Pre-processing filter=minimum 5 aminoacid length
  • Bayesian Score=norm primary score, deltaCn, secondary score, peaks matched, digestion score, presence score, secondary rank
  • Similar proteins=eliminate internal proteins
• General: group by charge state and group by number of enzymatic termini
• Acceptable FDR: spectra=5, peptide=3, protein=1 Post-processing quality filters= minimum one peptide per proteins, minimum one spectral count per protein

HorseTail (Equisetum hyemale)

• Description: Identification and quantification of proteins in the apical tip and elongation zone of rhizomes; and roots
• Protein extraction: Phenol-based protein extraction
• Pre-fractionation and protein digestion: 12%SDS-PAGE, in gel trypsin digestion
• Mass spectrometry data acquisition: LC-ESI-CID-MS/MS (LTQ), DDA experiment, fragmentation of top 7 peptide ions per cycle
• Peak list generator: extract_msn.exe
• Search algorithm: Sequest
• Database: translated EhRi (EhRi_unitrans_longest_rand.fasta):contigs+singles; 1assembly=1entry; 139,394 target+decoy entries
• Data filtering: SePro 1.0.0.46
• Parameters:
  • Pre-processing filter=minimum 5 aminoacid length
  • Bayesian Score=norm primary score, deltaCn, secondary score, peaks matched, digestion score, presence score, secondary rank
  • Similar proteins=eliminate internal proteins
• General: group by charge state and group by number of enzymatic termini
• Acceptable FDR: spectra=5, peptide=3, protein=1 Post-processing quality filters= minimum one peptide per proteins, minimum one spectral count per protein

Red Rice (Oryza longistaminata)

• Description: Identification and quantification of proteins in the apical tip and elongation zone of rhizomes; and roots
• Protein extraction: Phenol-based protein extraction Pre-fractionation and protein digestion: 12%SDS-PAGE, in gel trypsin digestion Mass spectrometry data acquisition: LC-ESI-CID-MS/MS (LTQ), DDA experiment, fragmentation of top 7 peptide ions per cycle
• Peak list generator: extract_msn.exe
• Search algorithm: Sequest
• Database: translated OlRi (OlRi_unitrans_longest_rand.fasta):contigs+singles; 1assembly=1entry; 91,460 target+decoy entries
• Data filtering: SePro 1.0.0.64
• Parameters:
  • Pre-processing filter=minimum 5 aminoacid length
  • Bayesian Score=norm primary score, deltaCn, secondary score, peaks matched, digestion score, presence score, secondary rank
  • Similar proteins=eliminate internal proteins
• General: group by charge state and group by number of enzymatic termini
• Acceptable FDR: spectra=5, peptide=3, protein=1
• Post-processing quality filters= minimum one peptide per proteins, minimum one spectral count per protein

• Description: Identification and quantification of proteins in the apical tip and elongation zone of rhizomes; and roots
• Protein extraction: Phenol-based protein extraction
• Pre-fractionation and protein digestion: 12%SDS-PAGE, in gel trypsin digestion Mass spectrometry data acquisition: LC-ESI-CID-MS/MS (LTQ), DDA experiment, fragmentation of top 7 peptide ions per cycle
• Peak list generator: extract_msn.exe
• Search algorithm: Sequest
• Database: translated ZoRi (ZoRi_unitrans_trans_rand.fasta):contigs+singles; 1assembly=1entry; 142,094 target+decoy entries
• Data filtering: SePro 1.0.0.51
• Parameters:
  • Pre-processing filter=minimum 5 aminoacid length
  • Bayesian Score=norm primary score, deltaCn, secondary score, peaks matched, digestion score,
  • presence score, secondary rank
  • Similar proteins=eliminate internal proteins
• General: group by charge state and group by number of enzymatic termini
• Acceptable FDR: spectra=5, peptide=3, protein=1
• Post-processing quality filters= minimum one peptide per proteins, minimum one spectral count per protein