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Table 1 Analysis conditions and number of identifications for each experimental approach

From: Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells

  TRAP3high vs control TRAP shRNA
  Phosphoproteomics analysis
(IPG 2.5–3.7)
Standard proteomics analysis
(IPG 3–10)
(IPG 3–10)
  Replicate #1 Replicate #2 Replicate #1 Replicate #2  
Nr. of unique peptides 6266 5771 79,410 81,851 97,153
Nr. of unique phospho-peptides 3325 3892 b b b
Nr. of unique proteins 1,704a 1,968a 8433 8447 9848
Nr. of unique genes 1,695a 1,957a 8309 8315 9189
  1. aFor phosphoproteomics analysis the reported numbers refer only to proteins found to carry phosphorylated amino acids, and their corresponding genes
  2. bNo phospho-peptides are reported because phosphorylation was not included as dynamic modification when searching the data